RetrogeneDB ID: retro_btau_1672

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:32927526..32928628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSBTAG00000016680
• Aliases: PPID, CYP-40
• Description: Peptidyl-prolyl cis-trans isomerase D [Source:UniProtKB/Swiss-Prot;Acc:P26882]

Sequence

>retro_btau_1672
ATGTTGCATCCATCCCCCAGGCTAAGCTCTCCAACCCCGGTAACCTCGGAGTCTTCTTCAATGTGGACATCGGAGGGGAG
CAAGTTGGTTGAATTGTCTTAGAATTGTTTGCAGATATTATACCCAAAACTGCAGAATTTTTGTGCATTGTATACAGGAG
AAAAAAGCACTGGACCCACCACAGGAAAACCTCCCTGTTTCAGAGGATGTCCTTTGCATTGAAATACTAAAAACTTGATG
ATTCAGGGTGGAGACTTCTCAAATCAGAATAGGACAGGTGGAGAAAGCATTTATGGTGAAAAACTTGAAGGTGAAAATTT
CTGTTATAAGCGTGACGAGGAGGGATTGCTGAGCATGGCCAAGCAGGCAGCAACACCAACGGCTTCCAGTTCATCACCAC
GGTTCTGACTCCACACTTGGATGGGAAGCACATAGTGTTTGGCCAAGGGATTAAAAAATGGGTGTGGCAAAGATTCTGGA
AAATGTGGAGGTGAAAGGTGAAAAACCTGCCAAATTTTGTGTTATTGCAGAATGTGGAAAACTGAAAGAAGGTGATGATT
GGAAAATATTCCCAAGGGATGGATCTGGTGACAGTCACCCAGATTTCCCCGAGGTTGCGGATGTGGATTTAAAAGATGTA
GATAAAATTGTGTTAATATCAGAAGACTTAAAAAACATTGGAAATACATTTTTCAAATCCCAGAACTGGAAGATGGCCAT
TAAAAAATACACAAAATTTTTAAGGTATGTGGAAGGCTCTAGGGCTGCTGCTGAGGACGCAAATGGAGCAAAGCTGTAGC
CTGTCGCTTTGAGCTGCATGCTGAATGTCAGCGCTTACAAACTGAAGATGTCCGATCGGCAGGGTGCAGTCGATAGCTGT
TTGGAGGCCCTTGAAATAGACCCATCAAATACCAAAGCACTGTACCGTAGAGCTGAAGGATGGCAAGGATTAAAAGAATA
TGTTCAAGCATTGGCTGATTTTAAGAAAGCTCAGGAGATAGCACCAGAAGATAAAGCTATCCAGGCAGAATTGCTGCAAG
TCAAGCAAAAGATGAAGGCACAGAAAGATAAAGAGAAGGCAGCTCATGCAAAAATGTTTGCT

Alignment

ORF - retro_btau_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSHPSP-QAKPSNPSNPRVFFDVDIGGERVGRIVLELFADIV-PKTAENFRALCTGEKGIGPTTGKPLHF
          M.HPSP.QAK.SNP.N..VFF.VDIGGE.VG.IVLELFADI..PK...NF.AL.TGEK..GPTTGKP..F
Retrocopy MLHPSP<QAKLSNPGNLGVFFNVDIGGEQVG*IVLELFADII>PKL-QNFCALYTGEKSTGPTTGKPPCF

Parental  KGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMAN-AGSNTNGSQFFITTV
          .GCP.H...K..MIQGGDFSNQN.TGGESIYGEK.E.ENF.YK.D.EGLLSMA..AGSNTNG.QF.ITTV
Retrocopy RGCPLH*NTKNLMIQGGDFSNQNRTGGESIYGEKLEGENFCYKRDEEGLLSMAK<AGSNTNGFQF-ITTV

Parental  PTPHLDGKHVVFGQVIKG-MGVAKILENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDFP
          .TPHLDGKH.VFGQ.IK..MGVAKILENVEVKGEKPAK.CVIAECG.LKEGDDW.IFP.DGSGDSHPDFP
Retrocopy LTPHLDGKHIVFGQGIKK<MGVAKILENVEVKGEKPAKFCVIAECGKLKEGDDWKIFPRDGSGDSHPDFP

Parental  EDADVDLKDVDKILLISEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCV
          E.ADVDLKDVDKI.LISEDLKNIGNTFFKSQNW.MAIKKYTK.LRYVEGSRAAAEDA.GAKL.PVALSC.
Retrocopy EVADVDLKDVDKIVLISEDLKNIGNTFFKSQNWKMAIKKYTKFLRYVEGSRAAAEDANGAKL*PVALSCM

Parental  LNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAE
          LN..A.KLKMSD.QGAVDSCLEALEIDPSNTKALYRRA.GWQGLKEY.QALAD.KKAQEIAPEDKAIQAE
Retrocopy LNVSAYKLKMSDRQGAVDSCLEALEIDPSNTKALYRRAEGWQGLKEYVQALADFKKAQEIAPEDKAIQAE

Parental  LLKVKQKIKAQKDKEKAAYAKMFA
          LL.VKQK.KAQKDKEKAA.AKMFA
Retrocopy LLQVKQKMKAQKDKEKAAHAKMFA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	22.57 RPM
ERP005899_muscle	0.00 RPM	55.22 RPM
SRP017611_brain	0.00 RPM	38.46 RPM
SRP017611_kidney	0.00 RPM	39.18 RPM
SRP017611_liver	0.00 RPM	20.46 RPM
SRP030211_testis	0.02 RPM	49.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1672 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1672 has 0 orthologous retrocopies within eutheria group .

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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,