CI01000026_07872070_07873313 (CLN6, CLN6A)


Basic Information

Item Value
gene id CI01000026_07872070_07873313
gene name CLN6, CLN6A
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000026
NCBI id null
chromosome length 17172400
location 7871575 ~ 7873357 (+)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000026_07872070_07873313.mRNA
CTATAAAAAAATCGATTAACCATGCGGAGAAGACCACAGTCTGCAGCTTTAACTCCGGCATATTTGAGGTCAGATTTTAATGCTTTCATGTTATCTAATATCACCATTTAATTGTGCAATATTACATGAACAGGTCACAGGGTAGTCGGGTGATTTACTGTGCTGTCAACATTTTAATTGGTCTGGCATTCGATTAAAATGACCTTTTTCCTAATGCACAGTCTGTATATTCAACAAAGACTAGCATTTCTAATGAAAATGCTGTACTTTTTAAAAAAGCAGGACTGGGAGTGAGAAAACAGTTTCAGCAGCAGCAGCACAGTCCCAGTTTCACACAGATCTCTGGCTCTGTTTCACTGTGCAAAACTGGATATTGGACTTTGGGAGGCCAATTGCTATGGTACAAGTTAAAACAAGGTGTGATCTATGCATTAAAATGTTCTTTCTCTTCTTTAATACCAATAACAACTTTGTATGTTCTTCATCTAGATCGTAATGCCTCTAGAATGGTTTCCTCTAAATAAACCAAGTGTTGGAGATTATTTTCACATGGCATATAATGTCATTACACCATTCTTATTACTGAAGCTGATTGAGCGGAGTCCCACGGCCCTTCCTCGCTCAGCAGTTTATCTCAGCATCATCACTTTTGTCATGGGAGCCAGCATACACCTAGTGGGAGACTCTATTAACCATCGTCTCATCCTCAGTGGATACCAGCTTCATCTTTCTGTCAGAGAGAACCCCATTATCAAGGATCTGAAGCCTACCTCACTGATTGATTCCTTTGAGCTTCTGTATTACTATGATGAGCACTTAGGGCATTGCATGTGGTATGTCCCATTCTTCCTCATCCTCTTCTTGTATTTCACTGGCTGCTTTACACAAGCTAAAGATGAGAGGATGCCTTACTCAGGTTGGCTGCTACTTGGCCCTAGTGCAGTGTACTATTGGTATCTGATTACTGAGGGGCAGATTTTTGTTCTGTATGTCTTCACCTTTTTTGCCATGGTTGCCACTGTGATGCGCCAGAGGCGGATGGGCTTCATGCTAGACAGCAATGGCTGTTTCCTCTTCTATAACTTCATCATTACTCTGGGGTTAGTTCTGGTTTGGGTCGCATATCTGTGGAATGATGAAGTTTTGCGCAAAAAGTATCCCGGTATCATCTATGTCCCTGAGCCGTGGTCCTTTTATACCTTACACATCAAAGGCAGTTAAATAACAACAGTAAATCTGAGCTACATTTCCGTGACGTTTCTCTA

Function

symbol description
cln6a Predicted to be involved in lysosome organization. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum and membrane. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis; neuronal ceroid lipofuscinosis 4A; and neuronal ceroid lipofuscinosis 6. Orthologous to human CLN6 (CLN6 transmembrane ER protein).
cln6 Enables lysophosphatidic acid binding activity; protein homodimerization activity; and sulfatide binding activity. Involved in several processes, including cholesterol metabolic process; ganglioside metabolic process; and lysosomal lumen acidification. Located in several cellular components, including early endosome; endoplasmic reticulum lumen; and membrane raft. Implicated in neuronal ceroid lipofuscinosis; neuronal ceroid lipofuscinosis 4A; and neuronal ceroid lipofuscinosis 6.

GO:

id name namespace
GO:0016021 integral component of membrane cellular_component

KEGG:

id description
K12359 CLN6; ceroid-lipofuscinosis neuronal protein 6

RNA

RNA id representative length rna type GC content exon number start site end site
CI01000026_07872070_07873313.mRNA True 1265 mRNA 0.41 5 7871575 7873357

Neighbor

gene id symbol gene type direction distance location
CI01000026_07766716_07782894 BBOX1 coding upstream 88583 7766716 ~ 7782992 (+)
CI01000026_07763144_07765276 FIBIN, FIBINB coding upstream 106239 7762708 ~ 7765336 (+)
CI01000026_07716356_07721570 TIPIN coding upstream 149970 7716356 ~ 7721605 (+)
CI01000026_07177994_07186042 NA coding upstream 684026 7177994 ~ 7187549 (+)
CI01000026_07160036_07169929 GLCEB, GLCE coding upstream 701244 7159592 ~ 7170331 (+)
CI01000026_07874837_07876094 CALL4, CALML4A, CALML4 coding downstream 1480 7874837 ~ 7876199 (+)
CI01000026_07900733_07907266 RFX7 coding downstream 27376 7900733 ~ 7908808 (+)
CI01000026_07911644_07954640 NA coding downstream 38287 7911644 ~ 7954640 (+)
CI01000026_07965621_07990576 SLC9A5 coding downstream 92219 7965576 ~ 7990643 (+)
CI01000026_08031599_08081760 PLEKHG4 coding downstream 158242 8031599 ~ 8081905 (+)
G130857 NA non-coding upstream 56709 7803928 ~ 7814866 (+)
G130843 NA non-coding upstream 84658 7785163 ~ 7786917 (+)
G130865 NA non-coding upstream 119802 7751567 ~ 7751773 (+)
G130864 NA non-coding upstream 121108 7750257 ~ 7750467 (+)
G130842 NA non-coding upstream 144908 7725309 ~ 7726667 (+)
G130910 NA non-coding downstream 3997 7877354 ~ 7877768 (+)
G130894 NA non-coding downstream 48817 7922174 ~ 7926132 (+)
G130962 NA non-coding downstream 301904 8175261 ~ 8176018 (+)
G130986 NA non-coding downstream 329484 8202841 ~ 8203962 (+)
G130993 NA non-coding downstream 343593 8216950 ~ 8217316 (+)
G130552 NA other upstream 774923 7095053 ~ 7096652 (+)
G128757 NA other upstream 1544790 6326196 ~ 6326785 (+)
G128601 NA other upstream 1879814 5983879 ~ 5991761 (+)
G128585 NA other upstream 1921453 5949813 ~ 5950122 (+)
CI01000026_04556074_04556964 FOXB1B, FOXB1, FOXB1A other upstream 3315258 4555776 ~ 4557613 (+)
G130967 NA other downstream 315017 8188374 ~ 8189073 (+)
CI01000026_08297901_08307596 CTRB1 other downstream 425216 8297857 ~ 8307629 (+)
G131077 NA other downstream 628051 8501408 ~ 8506787 (+)
G132667 NA other downstream 1695382 9568739 ~ 9569160 (+)
G133192 NA other downstream 2286462 10159819 ~ 10161961 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_033871 cln6a coding NC_007118.7 CM002891.2 34487833 ~ 34492609 (+)