RetrogeneDB ID: retro_itri_38

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393752.1:84815..85934(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000010267
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSSTOG00000005537
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_itri_38
ATGGGGCTCCGTAAGAAGGGCACCAAGAACCCCCCGGTGCTGAGCCAAGAATTCATCCTGCAGAATCATGCGGACCTCGT
CTCCTGCGTGGGGATGTTCTTCGTGCTGGGGCTCATGTTCGAGGGAACGGCCGAAGTGTCGATCGTTTTCCTCACTCTTC
AGCACAGCGTGGTGGTCCCTGCGGAAGAACTGGCTGCGGGATCCAAGACGCTGTATCATTACGGGGTCAAAGATTTGGCC
ACGGTCTTCTTCTACATGCTGGTGGTGATCATCATTCACGCCACGATCCAGGAGTACGTCCTGGATAAAATTAGCAGGAG
GATGCAGTTCACCAAAGCCAAACAGAACAAATTTAATGAATCTGGCCAGTTTAGTGTATTCTACATTGTCTCCTGTATCT
GGGGCACAATCATCCTCATGTCCGAAAACTGCCTGTCAGACCCCACTCTCCTGTGGAGGACTCATTCCCACACCATGATG
ACGTTTCAAATGAAGTTTTTCTACATCTCACAGTTGGCTTACTGGTTTCATGGTTTTCCGGAACTCTACTTCCAGAGAAT
CCGAAAACAAGATATCCCTAGTCAACTCATCTACATTGGTCTTCACCTCTTTCACATCACTGGAGCCTATCTCTTGTACT
TGAACCACCTGGGACTACTTCTGTTGGTGCTGCATTATTTCGTTGAATTGATTTCCCACCTGTGCGACGTGTTTTATTTC
AGTGATGAGAAGTACCAGAAGGGGGTTTCTCTGTGGACCATCGTGTTTGTCTTGGGGCGACTCACGACTTTAGTTGTTTC
ATTGGTCACTGTTGGGCTACACTTGGTTGTATCCCATTCCCGGGATGGGGATACGGATTCCATCAGTGGAAACGTCAACG
TGTTGGCGGCTGAAATCGCTGTTCTGTCGTCCAGTTGCACCATCCAAGCCTATATAACATGGACCTTACTGACAGTCTGG
CTTCAGAGGTGGCTAGAGGATTCTAATCTTCAGGCCTCGAGTCTGAAGAAGAAAAAACCCATGATTAAAGGCCGGTCTTC
TAGAAAAGGAACAGAAAATGGAGTGGAGACTGCAAACAGAGTAGATGCCCCGCCAAAGAGGAAAGAGAAAACTTCATAA

Alignment

ORF - retro_itri_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.61 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLTLTGILFEITAKASIIFVTLQYNVTLPATEEQATESASLYYYGIKDLATVFFYMLVAIIIHAIIQEYV
          M....G..FE.TA..SI.F.TLQ..V..PA.EE.A..S..LY.YG.KDLATVFFYMLV.IIIHA.IQEYV
Retrocopy MFFVLGLMFEGTAEVSIVFLTLQHSVVVPA-EELAAGSKTLYHYGVKDLATVFFYMLVVIIIHATIQEYV

Parental  LDKINRRMHFSKTKHSKFNESGQLSAFYFFACVWGTFILVSENYISDPTILWRAYPHNLMTFQMKFFYIS
          LDKI.RRM.F.K.K..KFNESGQ.S.FY...C.WGT.IL.SEN..SDPT.LWR...H..MTFQMKFFYIS
Retrocopy LDKISRRMQFTKAKQNKFNESGQFSVFYIVSCIWGTIILMSENCLSDPTLLWRTHSHTMMTFQMKFFYIS

Parental  QLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYF
          QLAYWFH.FPELYFQ...K.DIP.QL.YIGL.LFHI.GAYLL.LNHLGL.LLVLHYFVE...H....FYF
Retrocopy QLAYWFHGFPELYFQRIRKQDIPSQLIYIGLHLFHITGAYLLYLNHLGLLLLVLHYFVELISHLCDVFYF

Parental  SDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGL--ARAENQKLDFSTGNFNVLAVRIAVLASICITQA
          SDEKYQKG.SLW...FVLGRL.TL..S..TVG..L..........D...GN.NVLA..IAVL.S.C..QA
Retrocopy SDEKYQKGVSLWTIVFVLGRLTTLVVSLVTVGLHLVVSHSRDGDTDSISGNVNVLAAEIAVLSSSCTIQA

Parental  FMMWKFINFQLRRWREHSTFQAPPVRKKPTVTKGRSSRKGTENGVNGTVTSNGADSPRNRKEKSS
          ...W......L.RW.E.S..QA....KK....KGRSSRKGTENGV....T.N..D.P..RKEK.S
Retrocopy YITWTLLTVWLQRWLEDSNLQASSLKKKKPMIKGRSSRKGTENGVE---TANRVDAPPKRKEKTS

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_38 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_38 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 25 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Monodelphis domestica	ENSMODG00000007316	1 retrocopy	retro_mdom_308,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38 ,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,