RetrogeneDB ID: retro_itri_427

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:19029326..19029779(-)
• Located in intron of: ENSSTOG00000024173

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN1
• Ensembl ID: ENSSTOG00000023219
• Aliases: None
• Description: akirin 1 [Source:HGNC Symbol;Acc:25744]

Sequence

>retro_itri_427
CCCACGGAGTTCCAGGCGGCACTGCTGAGCCCCGGTTCCCCGGCTCTGCGCCCCTCTGCCCGGCCACACTCCCGCCTCCG
GCTCGGGGACGCGGAGCCACGGCCACCGACTGTCCAGCAGCCCTCCCGGACTGGCACCAAGCAGCTCCTTCCCACTCCGG
AGCAATTTTTTTCAGAACATAAAGCAAGAATATGATTGTTACCGAGGTGGAAACATTTAGAATTTGTTCTCAATCAGAGT
GAAGCTTGGACTTTGGAAAGACAGCCTCATTCCTCAGCACTCACAGCACCTGATTCTCCAGGTTCCCCCTGGATGAGGAA
GGACCGGCCCACCTTGACCTTTGGACAAATGGGAATAACATGTGAGAGGCTCTTAAAAGACTTTGTAGAGAAAATTCGGG
AGAAGTGTGAGCAAATCCTCAATACCAAACTAGCAGAACAGTATGAATCTTTT

Alignment

ORF - retro_itri_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.34 %
• Parental protein coverage: 77.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKRRRCAPLPGPTPGLRPPDAEPPPPLQ---TQTPPPTLQQPAPPGSERRLPTPEQIF-QNIKQEYSRYQ
          P.....A.L....P.LR.P.A.P...L........PPT.QQP...G....LPTPEQ.F.QNIKQEY..Y.
Retrocopy PTEFQAALLSPGSPALR-PSARPHSRLRLGDAEPRPPTVQQPSRTGTKQLLPTPEQFF>QNIKQEYDCYR

Parental  -RWRHLEVVLNQSEACTSESQPHSSALTAPSSPGSSWMKKDQPTFTLRQVGIICERLLKDYEDKIREEYE
          .RW.HLE.VLNQSEA.T.E.QPHSSALTAP.SPGS.WM.KD.PT.T..Q.GI.CERLLKD...KIRE..E
Retrocopy <RWKHLEFVLNQSEAWTLERQPHSSALTAPDSPGSPWMRKDRPTLTFGQMGITCERLLKDFVEKIREKCE

Parental  QILNTKLAEQYESF
          QILNTKLAEQYESF
Retrocopy QILNTKLAEQYESF

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_427 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_427 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 24 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004715	1 retrocopy	retro_btau_853,
Canis familiaris	ENSCAFG00000003186	4 retrocopies	retro_cfam_1099, retro_cfam_1915, retro_cfam_2086, retro_cfam_810,
Choloepus hoffmanni	ENSCHOG00000003010	3 retrocopies	retro_chof_1529, retro_chof_624, retro_chof_672,
Callithrix jacchus	ENSCJAG00000002309	3 retrocopies	retro_cjac_1460, retro_cjac_3694, retro_cjac_4071,
Cavia porcellus	ENSCPOG00000015419	1 retrocopy	retro_cpor_1232,
Dasypus novemcinctus	ENSDNOG00000000332	3 retrocopies	retro_dnov_1265, retro_dnov_1828, retro_dnov_509,
Dipodomys ordii	ENSDORG00000009324	2 retrocopies	retro_dord_121, retro_dord_436,
Equus caballus	ENSECAG00000012589	1 retrocopy	retro_ecab_108,
Erinaceus europaeus	ENSEEUG00000004136	3 retrocopies	retro_eeur_257, retro_eeur_422, retro_eeur_703,
Echinops telfairi	ENSETEG00000006751	1 retrocopy	retro_etel_336,
Homo sapiens	ENSG00000174574	1 retrocopy	retro_hsap_4692,
Gorilla gorilla	ENSGGOG00000006053	1 retrocopy	retro_ggor_2920,
Macropus eugenii	ENSMEUG00000011154	1 retrocopy	retro_meug_2030,
Monodelphis domestica	ENSMODG00000017703	1 retrocopy	retro_mdom_1466,
Mustela putorius furo	ENSMPUG00000014440	1 retrocopy	retro_mputfur_1389,
Mus musculus	ENSMUSG00000023075	1 retrocopy	retro_mmus_733,
Nomascus leucogenys	ENSNLEG00000011849	1 retrocopy	retro_nleu_2363,
Oryctolagus cuniculus	ENSOCUG00000005500	1 retrocopy	retro_ocun_140,
Otolemur garnettii	ENSOGAG00000007962	2 retrocopies	retro_ogar_445, retro_ogar_674,
Pongo abelii	ENSPPYG00000001511	2 retrocopies	retro_pabe_3137, retro_pabe_3646,
Sarcophilus harrisii	ENSSHAG00000017458	1 retrocopy	retro_shar_577,
Ictidomys tridecemlineatus	ENSSTOG00000023219	1 retrocopy	retro_itri_427 ,
Tarsius syrichta	ENSTSYG00000003345	1 retrocopy	retro_tsyr_139,
Tursiops truncatus	ENSTTRG00000002293	2 retrocopies	retro_ttru_1848, retro_ttru_513,