RetrogeneDB ID: retro_itri_319

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:6910320..6911024(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSSTOG00000027980
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_itri_319
ATGAGCTTCCTAAAGAGTTTCCCGCCACTGGGGCAGGATGAGGGGCTTCGGCAACAGCAGCCAGATACAGAGGCTGTGCT
GAATGGAAAGGAAAGGGCCTTGGTATTGGCGCTCTTTACATCGCAGAGAGCCGCCTGTCTTGGTTAGATGGTTCTGGATT
AGGATTCTCACTGGAATATCCCACCATTAGTTTACATTCAGTCTCCAGAGACCTAAATGCTTATCCTCGAGAGCATTTGT
ATGTTATGGTGAATGGCAAATTTGGAGAATAATCAAAAGAATCTCTTGCTGAAGAAGAGGAGGAAGATAGTGATGATGAT
GTTGAACCTATTACTGAATTTTGATTTGTGCCTAGTGATAAATCAGCATTGGAGGTGAGGTTCACTGCAATTTGTGAATG
CTAGGCTTTGCATCCAGATCCTGAGGATGAAGACTCAGATGATTATGATGGAGAAGAATATGATGTGGAAGCACATGAAC
AAAGGCAGGGAGGTATTCCTACATTTTACACCTATGAAGAAGGATTATCCCATTTAACAGCAGAAGGGCAAGCCACACTG
GAGAGACTAGAAGGAATACTTTCTCAGTTTGTGAGCAGCCAGTGTAACATGGCTGGGGTCGGCACGGAAGATTCAGTAAG
AGATTATGAAGATGGCATGAAGATAGACACCACACCAACAGTTGCTGAGGATGCAGATGTTGAT

Alignment

ORF - retro_itri_319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.54 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFLKSFPPPGQDEGLRQQQPDTEAVLNGK-GLG--IGTLYIAESRLSWLDGSGLGFSLEYPTISLHAVS
          MSFLKSFPP.GQDEGLRQQQPDTEAVLNGK.G.G..IG.LYIAESRLSWLDGSGLGFSLEYPTISLH.VS
Retrocopy MSFLKSFPPLGQDEGLRQQQPDTEAVLNGK<GKGLGIGALYIAESRLSWLDGSGLGFSLEYPTISLHSVS

Parental  RDLNAYPREHLYVMVNAKFGEESKESLADEEEEDSDDDVEPITEFRFVPSDKSALEVMFTAMCECQALHP
          RDLNAYPREHLYVMVN.KFGE.SKESLA.EEEEDSDDDVEPITEF.FVPSDKSALEV.FTA.CEC.ALHP
Retrocopy RDLNAYPREHLYVMVNGKFGE*SKESLAEEEEEDSDDDVEPITEF*FVPSDKSALEVRFTAICEC*ALHP

Parental  DPEDEDSDDYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRT
          DPEDEDSDDYDGEEYDVEAHEQ.QG.IPTFYTYEEGLSHLTAEGQATLERLEG.LSQ.VSSQ.NMAGV.T
Retrocopy DPEDEDSDDYDGEEYDVEAHEQRQGGIPTFYTYEEGLSHLTAEGQATLERLEGILSQFVSSQCNMAGVGT

Parental  EDSVRDYEDGMEVDTTPTVAGQFEDADVD
          EDSVRDYEDGM..DTTPTVA...EDADVD
Retrocopy EDSVRDYEDGMKIDTTPTVA---EDADVD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_319 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_319 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319 , retro_itri_490,