RetrogeneDB ID: retro_itri_32

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393349.1:619873..623191(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019572
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSSTOG00000011164
• Aliases: None
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_itri_32
ATGGCGGCGGCCGGGTCTGCAGGGGTGCCGGCGATTGTGTCGGAAAAGCAAGAGTTCTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGCATGGTGCGGAGGCAAGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACATTCCTCT
TAGATGCCGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGCCGGCTTTTGTCCTCT
GGGTTTGAGGAGGTCTACCCAAATCTGCCTTCTGATGTTCAGAGAGATGTCAAGATTGAACTGATACTGGCTGTTAAGTT
AGAAACACATGCTAGCATGAGGAAAAAGCTCTGTGATATTTTTGCGGTGCTGGCCAGGAATTTGATAGATGAGGATGGCA
CTAACCATTGGCCAGAAGGTCTGAAGTTCCTTATTGATTCGATCTACTCTAAAAATGTGGTTCTGTGGGAAGTTGCACTT
CACGTCTTCTGGCACTTTCCTGGAATTTTTGGGAACCAAGATCGGCACGATTTGGATATCATCAAAAGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCTGCTAGAGCTGCAGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAAGCTGTCAATGATTCATGCTACCAGGAT
GATGATTCAGTGCTAGAATCCCTTGTTGAGATTGCTGATACAGTACCTAAATATTTGGGTCCTTATTTAGAAGATACTCT
ACAGTTGAGCCTGAAGTTATGTGGAGATTCTAGACTTAGTAACCTGCAACGCCAGCTGGCCCTTGAAGTAATAGTGACCT
TGTCTGAAACTGCAACTCCAATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCTCTAGACAGACTGGCTTGTGGGCTTGGTGGAAAAGTTGTTTTACCAATGACCAAGGAGCATATCATGCAAA
TGCTTCAGAGCCCTGACTGGAAGTATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGTTGTCATCAGCAA
ATGGAACCAATTCTAGATGAAACTGTTAACTCTGTTTTACTTTTTCTTCAGGATCCTCATCCAAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAAATGGCTACAGATTTTGCACCTAGTTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTT
TGTTGCGTACGATGGAAAATCAAGGTAATCAGCGTGTACAATCTCATGCAGCTTCTGCTCTTATTATTTTTATTGAAGAT
TGCCCCAAGTCATTATTAGTTCTCTATTTGGATAGTATGGTGAAAAATCTACATTCTATCTTGGTGATTAAACTTCAAGA
GTTGATTCGGAATGGAACTAAGTTGGCCTTGGAACAGCTTGTGACAACCATTGCCTCAGTTGCAGATACGATAGAAGAAA
AATTTATTCCATATTATGACATATTTATGCCCTCACTAAAGCATATTGTTGAGCTTGCTGTTCAGAAGGAACTCAAGCTT
CTGAGAGGAAAAACTATTGAGTGCATTAGCCATGTTGGTCTTGCTGTTGGGAAGGAAAAATTTATGCAAGATGCATCAAA
TGTGATGCAGCTATTGTTGAAGACACAATCAGACTTGAATAATATGGAAGATGATGACCCTCAGACCTCTTACATGGTTT
CAGCTTGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTCCAACAGTACCTTCCACTGGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTCGCTCTCTTAGACACACAAGATGTAGAGAATATGAGTGATGATGATGGATGGCAATT
TGTAAATCTTGGAGACCAGCAGAGTTTTGGAATTAAAACTTCTGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGCTGG
TTTACTATGCTAAGGAGTTAAGAGAAGGATTTGTGGAGTATACAGAACAAGTTGTGAAATTAATGGTTCCCTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCTGCAGAGTCCATGCCTTTTCTCCTGGAATGTTCAAGAATTCGTGGTCC
AGAGTATCTTTCACAGATGTGGCAGTTCATATGTGACCCCTTAATCAAGGCTATAGGAACTGAACCTGATACTGATGTAC
TCTCAGAAATAATGAATTCTTTTGCAAAGTCCATTGAGGTAATGGGAGATGGTTGCCTCAATGATGAACACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAACTTGAAGGACATTTTAAAAACCAAGAATTACGACAGGTTAAAAGACAAGAAGAAAA
CTATGACCAACAGGTTGAGATGTCTCTGCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTATAAAGAAAAGATTTTACCATGGTTTGAACAGCTGCTTCCATTAATTGTAAATCTAATA
TGTTCAAGTAGACCATGGCCAGACAGACAGTGGGGATTATGCATATTTGATGATATCATAGAGCACTGTAGCCCAACCTC
ATTTAAATATGTAGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGATAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTCTATGTTCAGAAGCTGTTCCACTACTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCGACAGAGAACTGCATCTCAGCAATAGGGAAGAT
TTTGAAGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAAGATA
AAGAGGAAGCGATTCAGACTTTGAGTTTTCTCTGTGACTTAATTGAAAGTAACCACCCAGTTGTAGTTGGTCCAAATAAT
TCTAATCTCCCCAAAATAATTAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAGCTATGAAGATCCTTGTGCCAA
ACGCCTTGCTAATGTTGTTCGTCAGGTACAAACATCTGAAGAATTATGGTCAGAATGTATATCGCAACTTGATAATGAAC
AGCAGGAAGCCTTACAGGAATTGCTAAATTTTGCTTGA

Alignment

ORF - retro_itri_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQNPDWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQ
          MLQ.PDWKYRHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQ
Retrocopy MLQSPDWKYRHAGLMALSAIGEGCHQQMEPILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPSFQ

Parental  KKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQELIQKGT
          KKFHE.VIAALL.TME.QGNQRVQ.HAA.ALI.F.EDCPKSLL..YLD..VK.LHSI.V.KLQELI..GT
Retrocopy KKFHETVIAALLRTMENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDSMVKNLHSILVIKLQELIRNGT

Parental  KLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQ
          KL.LEQ.VT.IASVADT.EEKF.PYYD.FMPSLKHIVE.AVQKEL.LLRGKTIECIS..GLAVGKEKFMQ
Retrocopy KLALEQLVTTIASVADTIEEKFIPYYDIFMPSLKHIVELAVQKELKLLRGKTIECISHVGLAVGKEKFMQ

Parental  DASDVMQLLLKTQTDFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDT
          DAS.VMQLLLKTQ.D.N.MEDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.KTAS.KP.VALLDT
Retrocopy DASNVMQLLLKTQSDLNNMEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIKTASAKPDVALLDT

Parental  QDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYF
          QD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLMVPLLKFYF
Retrocopy QDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVKLMVPLLKFYF

Parental  HDDILYSTAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIEVMGDGCL
          HD......AESMP.LLEC.R.RGPEYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM.SFAK.IEVMGDGCL
Retrocopy HDNVRVAAAESMPFLLECSRIRGPEYLSQMWQFICDPLIKAIGTEPDTDVLSEIMNSFAKSIEVMGDGCL

Parental  NNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHSIFSSYKE
          N.EH.EELGGILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKVSDILHS.FS.YKE
Retrocopy NDEHLEELGGILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKVSDILHSLFSTYKE

Parental  KVLPWFEQFLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVCDNSPEVRQAA
          K.LPWFEQ.LPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML....DN.PEVRQAA
Retrocopy KILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLLNMRDNNPEVRQAA

Parental  AYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIMKYKPDCVNVEEVLPH
          AYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISA.GKI.K.KP.CVNV.EVLPH
Retrocopy AYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAIGKILKFKPNCVNVDEVLPH

Parental  WLSWLPLHEDKEEAVQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGELHEAIKHEDPCAKRLANVV
          WLSWLPLHEDKEEA.QT...LCDLIESNHP.V.GPNN.NLPKI.SIIAEG...E.I..EDPCAKRLANVV
Retrocopy WLSWLPLHEDKEEAIQTLSFLCDLIESNHPVVVGPNNSNLPKIISIIAEGKINETISYEDPCAKRLANVV

Parental  RQVQTSGGLWTECIAQLSPEQQAAIQELLNSA
          RQVQTS..LW.ECI.QL..EQQ.A.QELLN.A
Retrocopy RQVQTSEELWSECISQLDNEQQEALQELLNFA

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_32 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_32 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 21 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003784	1 retrocopy	retro_amel_3,
Bos taurus	ENSBTAG00000039374	1 retrocopy	retro_btau_104,
Canis familiaris	ENSCAFG00000005561	1 retrocopy	retro_cfam_452,
Choloepus hoffmanni	ENSCHOG00000006061	1 retrocopy	retro_chof_11,
Cavia porcellus	ENSCPOG00000004827	2 retrocopies	retro_cpor_265, retro_cpor_57,
Equus caballus	ENSECAG00000014808	1 retrocopy	retro_ecab_37,
Felis catus	ENSFCAG00000025657	1 retrocopy	retro_fcat_24,
Homo sapiens	ENSG00000065150	1 retrocopy	retro_hsap_57,
Gorilla gorilla	ENSGGOG00000008742	1 retrocopy	retro_ggor_47,
Loxodonta africana	ENSLAFG00000016190	1 retrocopy	retro_lafr_22,
Myotis lucifugus	ENSMLUG00000006500	1 retrocopy	retro_mluc_295,
Mus musculus	ENSMUSG00000030662	2 retrocopies	retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys	ENSNLEG00000007831	2 retrocopies	retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus	ENSOCUG00000003898	1 retrocopy	retro_ocun_143,
Otolemur garnettii	ENSOGAG00000007570	1 retrocopy	retro_ogar_169,
Pongo abelii	ENSPPYG00000005458	1 retrocopy	retro_pabe_172,
Pan troglodytes	ENSPTRG00000005984	2 retrocopies	retro_ptro_49, retro_ptro_745,
Pteropus vampyrus	ENSPVAG00000004516	1 retrocopy	retro_pvam_8,
Rattus norvegicus	ENSRNOG00000010989	1 retrocopy	retro_rnor_240,
Sus scrofa	ENSSSCG00000009509	1 retrocopy	retro_sscr_24,
Ictidomys tridecemlineatus	ENSSTOG00000011164	1 retrocopy	retro_itri_32 ,