RetrogeneDB ID: retro_itri_1502

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393515.1:1363726..1364121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSSTOG00000027396
• Aliases: None
• Description: cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]

Sequence

>retro_itri_1502
TTGTTCATCTTGCTCCTCAATTTTGCACTAGTCATCCTCAGTCTATTCCTAATTATATTGTCTGATTTAGAGCGTAATTA
CATTAGTGCTAGATCATGTTTCTCAAAATTAAACAAGTGGGTAATTCCAGAATTGATAGGCCTTATCACTGTTGCTGTAT
TGATGCTTGTTTCATTGTACTGGTCCCTATTCCTTCTTAACTTAGATGTTGCTACTTGAAATACGTATCAGTCATTACGG
TGCCAAGTGGCAGCATGTGAGTGTTTGATCCAACAGAAGTACACAAGCAAGTTCAATCGAAGACACATGTGAAAGAAGCC
ATGATCAAGCTTGGTTTCCACTTGCTCTGTTTCTTCATGAATCTTTACAGTATGCTTTTAGCTTTGATAAATGAT

Alignment

ORF - retro_itri_1502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.15 %
• Parental protein coverage: 95.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFSLLDCCALIFLSVYFIITLSDLECDYINARSCCSKLNKWVIPELIGHTVVTVLMLVSLHWFIFLLNLP
          .F.LL...AL..LS...II.LSDLE..YI.ARSC.SKLNKWVIPELIG...V.VLMLVSL.W..FLLNL.
Retrocopy LFILLLNFALVILSLFLII-LSDLERNYISARSCFSKLNKWVIPELIGLITVAVLMLVSLYWSLFLLNLD

Parental  VATWNIYR-FIMVPSGNMGVFDPTEIHNRGQLKSHMKEAMIKLGFHLLCFFMYLYSMILALIND
          VAT.N.Y...I.VPSG.M.VFDPTE.H...Q.K.H.KEAMIKLGFHLLCFFM.LYSM.LALIND
Retrocopy VAT*NTYQ<VITVPSGSM*VFDPTEVHKQVQSKTHVKEAMIKLGFHLLCFFMNLYSMLLALIND

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_1502 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1502 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.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502 , retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,