RetrogeneDB ID: retro_itri_1422

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393482.1:2115047..2115903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSSTOG00000001552
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_itri_1422
CCCATCCCCCAAGCTAAAGCTTCCAGTCCCAGGAACCCATGAGTCTTCTTTGATGTGAACATCAGAGAGGAGCAAATTGG
CTGAATTGTCTTACAATTGTTTGTGGATATTGTACCCAAAACTGCAGAAAAATTTCGTGCATTGTGTACAGGAGAAAAAG
GCATTGGACCCATCACTGGGAAACCTCTTTATTTCAAAGTATGTCCTTTTCATTGAATTATTAAGGAATTTATGGTTCAG
AGTGGAGACTTCTCAAATCAGAATGGGACAGGTGGAAAAAGTATTTATGGTAAAATCTTTGAAGATAACAATTTCTACTA
TAAGCATGCTCAGGAAGGTTTACTGAACATGGCAAATACAGATAGCTATACAAATGGTTCTCAGTTCTTTATCACCAAGG
TCCAACCCCTCATTTGGATGTAAAATGCGGTGTTGGGTTAAGTACTTAAAAGAGTAGGTATGGCAAAGATACTGGAAAAT
ATAGAAGTGAAAGGTGAAAAACCCTCCACATTATGTGTTATTGCAGAATGTGGAGAACTGAAAAGGGGGATGTTTGGGGA
ATATTCCTAAAAGAAGCTCTGGCTATAGTCATCCAGATTTCCCTAAGAATATAGATGTAGACTAAAAAGATGTAGATAAA
ATTTTATTAATAATAGAACACTTAAAAAACATTGGATATACTTTTTTTTTTTCCAAATCCCAACACTGGGATATGACCAT
TAAAAAATTAGCAAAGGTTTAAACATATGTGGATAGTTCAAAGGCTGTTATTGAGAAAGCAGGTAGATCCAGGCTGCAAT
CTATAACCTTAAGCTGTGTACTGAACATTGGTGCTTGTAAAGTAAAAATTGCTTCC

Alignment

ORF - retro_itri_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSPEAKPSNPSNPRVFFDVDIGEERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLYFKGCPF
          P.P.AK.S.P.NP.VFFDV.I.EE..G.IVL.LF.DIVPKTAE.FRALCTGEKGIGP.TGKPLYFK.CPF
Retrocopy PIPQAKASSPRNP*VFFDVNIREEQIG*IVLQLFVDIVPKTAEKFRALCTGEKGIGPITGKPLYFKVCPF

Parental  HRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFYYKHDREGLLSMANAGRNTNGSQFFITTVPTPHLD
          H.IIK.FM.Q.GDFSNQNGTGG.SIYG..FED.NFYYKH..EGLL.MAN....TNGSQFFIT.V..P...
Retrocopy H*IIKEFMVQSGDFSNQNGTGGKSIYGKIFEDNNFYYKHAQEGLLNMANTDSYTNGSQFFITKVQ-PLIW

Parental  GKHVVFGQVIKGIGVARMLENVEVKGEKPVKLCVIAECGELK-EGDDWGI-LPKDGSGDSHPDFPEDADI
          ....V.G.V.K..G.A..LEN.EVKGEKP..LCVIAECGELK..GD.WGI..PK..SG.SHPDFP...D.
Retrocopy M*NAVLG*VLKRVGMAKILENIEVKGEKPSTLCVIAECGELK<KGDVWGI<IPKRSSGYSHPDFPKNIDV

Parental  DLKDVDKILLITEDLKNIG--NTFFKSQNWEMAMKKYAKVLRYVDSSKAVIEKADGSRLQSIALSCVLNI
          D.KDVDKILLI.E.LKNIG......KSQ.W.M..KK.AKV..YVDSSKAVIEKA..SRLQSI.LSCVLNI
Retrocopy D*KDVDKILLIIEHLKNIGYXXXXXKSQHWDMTIKKLAKV*TYVDSSKAVIEKAGRSRLQSITLSCVLNI

Parental  GACKLKMSN
          GACK.K...
Retrocopy GACKVKIAS

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_1422 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1422 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422 ,