RetrogeneDB ID: retro_itri_726

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:12842424..12843321(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000029189
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A15
• Ensembl ID: ENSSTOG00000007840
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 [Source:HGNC Symbol;Acc:10985]

Sequence

>retro_itri_726
ATGAAGTCCAGCCCCAGCATCCAGGCTGCCATCGACCTCACAGCCGGGGCCGCAGGGGGTACAGCGTGTGTACTGACTGG
GCAGCCCTTTGACACAATGAAAGTGAAGATGCAGACATTCCCTGGCCTGTACACGGGCCTCAGAGACTGCTTCCGAAAGA
CATACAACCAAGTGGGTATCCGGGGCTTCTACAGGGGAACCTGCCCAGCACTGATGGCCCAAGTTTCCCAGAGCTCTGTC
CTCTTCATGTGCTACGGCTTTAGTCAACAGTTTGTTCGAAAAATGGTTGGCTTGGACAAGCAGGCAGAACTGAATGATCT
GCAGACTGCAACTGCCGGTTCCTTTGCCTCTGCGATTGCTGCCCTGGTCCTTTGCCCCACTGAGCTTGTGAAGTGCCGGC
TGCAGACCATGTATGAAATGGAGTTGTCAGGAAAGATAGTAAAAAGCCATAACACAATTTGGTCTGTCGTGAAGAGTATC
CTTAAGAAGGATGGTGTCTTAGGTTTATACCATGGTCTCTCAAGCACTCTACTTCAGGAAGTAATGGGCTATTTCTTCTT
CTTCGGTGGGTATGAACTGAGCAGATCTTTTTTTGCATCAGGGAGACCAAAGAATGAACTAGGCCCTGTCCCTTTGATGT
TAAGTGGTGGAGTTGCTGGAATCTGCCTCTGGCTTGTTGTATTCCCAGTGGATTGTATTAAATCCAGAATTCAGGTTCTT
TCCATGTATGGAAAACAGGCAGGATTTATTGGAACCTTGTTAAATATCGTGAGAAACGAGGGAGTACTAGCCTTATATTC
AGGACTGAAAGCTACCATGATTCGAGCATTCCCTTCCAATGGTGCACTATTTTTGGCCTATGAATACAGCAGGAAAACCA
TGATGAGCAACTTCGAA

Alignment

ORF - retro_itri_726 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.27 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKS.P.IQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFP.LY.GL.DC..KTY.QVG.RGFY.GT.PA
Retrocopy MKSSPSIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPGLYTGLRDCFRKTYNQVGIRGFYRGTCPA

Parental  LIANIAENSVLFMCYGFCQQVVRRAVGLDRQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A.....SVLFMCYGF.QQ.VR..VGLD.QA.L.DLQ.A.AGSFASA.AALVLCPTELVKCRLQTMYEM
Retrocopy LMAQVSQSSVLFMCYGFSQQFVRKMVGLDKQAELNDLQTATAGSFASAIAALVLCPTELVKCRLQTMYEM

Parental  ETSGKIARSQNTVWSVVKTILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SGKI..S.NT.WSVVK.IL.KDG.LG.YHGLSSTLL.EV.GYFFFFGGYELSRSFFASGR.K.ELGPV
Retrocopy ELSGKIVKSHNTIWSVVKSILKKDGVLGLYHGLSSTLLQEVMGYFFFFGGYELSRSFFASGRPKNELGPV

Parental  PLMLSGGIGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIGTFLGVVKNEGITALYSGLKPTMIRAFPAN
          PLMLSGG..GICLWL.V.PVDCIKSRIQVLSM.GKQAGFIGT.L..V.NEG..ALYSGLK.TMIRAFP.N
Retrocopy PLMLSGGVAGICLWLVVFPVDCIKSRIQVLSMYGKQAGFIGTLLNIVRNEGVLALYSGLKATMIRAFPSN

Parental  GALFLAYEYSRKLMMSQLE
          GALFLAYEYSRK.MMS..E
Retrocopy GALFLAYEYSRKTMMSNFE

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_726 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_726 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726 ,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,