RetrogeneDB ID: retro_btau_1639

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:23408784..23412320(-)
• Located in intron of: ENSBTAG00000038181

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.103213
• Ensembl ID: ENSBTAG00000012749
• Aliases: None
• Description: None

Sequence

>retro_btau_1639
GCTAGGACCTGGAACCAGATCCTTTTCTCACTAAGCCAGCAAGAGGCCATTGAGAAACACCTGGATTTTGACAGCTGCTG
TGCTCTGCTGGCACTGTTTGCACAGGCCATGCTCTCTGAACACCCGTTGTCTTTTGAGAGCATTCAGCTTCCACAGGTCC
CAGGAAGGCTGCTCTTCTCCCTGGTGAAGCGCTATTTGCATGTCACCTTCCTCCTGGATCAGTTGAATGACACTGCTGCA
GAACCAGGAGCCCCGCACTCCACTCCTGAGGAGCTGAGTGGGGAGAGGGGTCGCCTGGAGCTGGAGTTCAGCAAGGCTGT
GGGCACGCTGATCTCAGAGCTGGTGCAGGCCATGCGCTGGGACCAGGCCTGGAGCAGACAGGGGTCCTCAGGATAGCCCT
CCAGTTCCATCTTCCAGCCCCAGCTGGTGGATGAGGGCCCAGGGCTCCCATCTGCCCAGGCCTTGCCTTCCTGCAGGAGG
TCAAGGAGGTTTTGACCTCGCTCTGAGTTCGCAAGTGGCAATACCTATGCCTTGTACACGCGGGATGCACTGCAGCCGGG
CATGCGAGTGTGGATGCTGGATGACTATGAGATCAGCGTGGGCGACGAGGGCAAATTCCGGCAGAGCAACAATGGCGTGC
CCCCGTGCAGGTGCTGTTGGAGTCAACAGGCCGCACCTGTTGGCTGTACTGGCACATGCTGGAGATTCTGGGCTTGGAGG
AAGACATTGAGAACATGGTTGAGGCTGCTTATAAGTACCAGGGGGCAGTGGTCAGTGCAGCCATGGGTACAGCCCTGCCG
TACTGGCACTGGAAGCCCATGACCGAGCTCTATGCTGTGCCCTACGTGTGGCCTGCGGACGAGGACACTGAGGAGAGTGA
ACACCTGACCCAGGCCGAGTGGTGGGAGCTCCTCTTCTTCTTCAAGAAGCTGGATGGCCCCAACCATCAGGAGGTTCTCC
ATATCCTTCAGGAGAACCTGGACAGGGAGGTTCTGGATGACGAGATCCTGGCTGAACTGGCTATGCCCACGGAGGTGGCC
CAAGACCTGCTGCTGGCTCTGCCACAGCGACTTGACAACAGAGCCCTCAGGGATGTGCTCAACTGCCGCGTCTACAGGAA
GTACGGCCTGAGGCCCTGGCAGGGCAGCCGGCCCACCCATCCCTACTGGAAGCCTGGGCCCAGCCTCAGGAATCAGCTGA
CGCAGCCAGAGTGGAAGCAAAAGAAGCCCCAACTCAGGGCTCCAACACACTGCTGCAGCATCTGGCAGAGGGTTTCGGTC
CAGCTGGGAAAGTCTTCCTGGATCTGGAGGGAGCGTTCCACTCAGAGGGGGCCCCGGCAGGGAGAGGCCAAGCCCCTCCT
CCTGCAACTGCAGAGGCAGCCCCAGCCCTTCCTCGTGCTCATGCGGAGCCTCAACACTCCTGCCGCCAACAAGCCCCTGC
ACCTGGCTGTTCTGAGAATCCTGATGCAGCTGGTGGATTTCCCTGAGGCACTACTGCTCCCCTGGCATGAAGCTATGGAC
ACCTGCATGGCCTGCCTGCAGTCCCCAAACACTGACCGAGAGGTGCTCCAGGAGCTGATCCTCTTCCTGCACCGCCTGGC
CTCCATAAGCAGGGACTATGCCGTGGTGCTCAATCAGCTGGGAGCCCGGGATGCCATCTCCAAGGCTCTGGAAAAGCACC
TGGGAGAGCTGGAGCTGGCTCAGGAGCTGCGGGACATGGTATTCAAGTGTGAGAAGCATGCCCACCTCTACCGGAAGCTC
ACCACCAACATCCTGGGAGGCTGTATCCAGATGGTGCTGGGCCAGATTGAAGACCACAGACGAACCCACCACCCCATCAA
CATCCCCTTCTTCAATGTGTTCCTCAGATACCTGTGCTAGGGCTCTAGCATGGAGGTGAAGGAGGACAAGTGCTGGGAGA
AGGTGGAGGTGTTGTCCAACCTGCACTGGGCCAGCAAGCTGACGGACCGCAACCCCAAGACCTACTGGGAGTCCAACGGC
AGTGCCGGCTCCCACCACATCACCCTGCACATGCAGCAGGGCATCCTCATCAGGCAGCTGGCTCTTCTGGTGGCTAGCGA
GGACTTGAGCTACATGCCGGCCAGGGTGGTGGTGTTCGGGGGCGACAGCACCACCTCCCTTAACACGGAACTCAACTCGG
TGAACGTGATGCCCTCCGCCAGCCAGGTGGTCCTCCTGGAGAACCTGAGCCGCATCTGGCCCATCATCCAGATCCGCATA
AAGCGCTGCCAACAGGGCGGCATTGACACGTGTATTTGGGGGTTGGAGGTCCTGGGCCCCAAGCCCACGTTCTGGCCGGT
GTTCCGGGAGCAGCTGTGCCGCCACACACGCCTCTTCTACATGGTCCAGGCGCAGGCTTGGAGCCAGGACATCGTGGAGG
ACCACAGGGGACTCCTGCACCTGAGCTCCAGACTCAACGGGGCCCTACGCCACGAGCAGAACTTTGCTAGTCACTTCCTC
CCTGACGAAGAGGCCGCCCAGGCACTGGGCAAGACCTACTGGGAGGCCTTGGTCAGCCCCCTGGTGCAGAACATCACCTG
CCCTGATGAAGAAGGCGTCAGCCCCCTGGGCTGGCTGTTGGACCAGTACCTGGAGTGTCAGGAGCCTGCCCACAACCCGC
AGAGCCACGCGGCAGCGTTCTCCTCCTGGGTGTGCCGCATCACCCACCTGCTGGTGCACATGGAGCCCTGTGAAGCGCCC
CACTTGGTGGCGGCCTCGCCTCGGCCCAAGGGCAGAAACAGAAGCCACGACTGGAGCTCCCTGGCCACCCGGGGGCTTCC
CAGCAGCATCATGAGAAACCTGACGCACTGCTGGCGGGCGGTGGTGGAGGAGCAGGTGCACAGCTTTCTGACCTCATGCT
GGCAGGACGATGACTTTGTGCCCCACTACTGTGAACACTTCGGTAATCTGCAGAAGGCGAGCTCTGAGCTGTTTGGGCCA
CGGGCAGCCTTCTTGCTGGCGCTGCAGAATGGCTGTGCCGGTGCCCTGCTGAAGCTGCCTTTCCTCAGAGCTGGCCACGT
GAGCGAGCAGTTTGCCCAACACATCGACCAGCGGATCCAGGGCAGCTGGATCGGTGGGGCACGGGGAATGGAGATGCTGG
CCCAACTGCAGCTATGCCTGGAAACCATCCTCATCTTCTCTGGTCTGGAGATAGCCACTACTTTCAAGCATTACTACCAG
CACTACATGGCGGACCGTCTCCTGGGCGTGGGCTCGAGCTGGCGGGAGGGGGCCGTGCTGGAGCAGATCGGCCCCTGCTT
CCCCAACCGCCTCCCCCAGCAGATGTTGCAGAGCCTGAGCACCTCAGAGGAGCTGCAGCACCAGCTCCACGTATACCAGC
TCCAGCGGCTTGATCAGGAACTCCTGAAGCTGGAGGACACAGAGAAGAAGATACAGGTGAGCCGTGACGCCAGTGGCAGG
GGCCATGAGAGAGGGACTGGGGAGGAAGCTGAGCTGGAAGCTGCGGCCTTGGCAGCAGCAGCAACAGCCAGCGTGGCGGG
GGAGGAGGAGTAGGAG

Alignment

ORF - retro_btau_1639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRTRTQILFSLSQQEAIEKHLDFDSRCALLALFAQATLSEHPMSFEGIQLPQVPGRLLFSLVKRYLHVTF
          .RT..QILFSLSQQEAIEKHLDFDS.CALLALFAQA.LSEHP.SFE.IQLPQVPGRLLFSLVKRYLHVTF
Retrocopy ARTWNQILFSLSQQEAIEKHLDFDSCCALLALFAQAMLSEHPLSFESIQLPQVPGRLLFSLVKRYLHVTF

Parental  LLDQLNDTAAEPGAPNSTPEELSGERGRLELEFSMAMGTLISELVQAMRWDQVWSRQGPSGQPSGSIFQP
          LLDQLNDTAAEPGAP.STPEELSGERGRLELEFS.A.GTLISELVQAMRWDQ.WSRQG.SG.PS.SIFQP
Retrocopy LLDQLNDTAAEPGAPHSTPEELSGERGRLELEFSKAVGTLISELVQAMRWDQAWSRQGSSG*PSSSIFQP

Parental  QLVDEGPGLPPAQALPSRRRSRRFRPRSEFASGNTYALYVRDALQPGMRVRMLDDYEEISAGDEGEFRQS
          QLVDEGPGLP.AQALPS.RRSRRF.PRSEFASGNTYALY.RDALQPGMRV.MLDDYE.IS.GDEG.FRQS
Retrocopy QLVDEGPGLPSAQALPSCRRSRRF*PRSEFASGNTYALYTRDALQPGMRVWMLDDYE-ISVGDEGKFRQS

Parental  NNGVPP-VQVLWESTGRTYWVHWHMLEILGFEEDIENMVEAADEYQGAAVSAAVGTALPSWRWKPMTELY
          NNGVPP.VQVL.ESTGRT.W..WHMLEILG.EEDIENMVEAA..YQGA.VSAA.GTALP.W.WKPMTELY
Retrocopy NNGVPP<VQVLLESTGRTCWLYWHMLEILGLEEDIENMVEAAYKYQGAVVSAAMGTALPYWHWKPMTELY

Parental  AVPYVWPEDEDTEESEHLTQAEWWELLFFIKKLDGPDHQEVLQILQENLDGEVLDDEILAELAVPTELAQ
          AVPYVWP.DEDTEESEHLTQAEWWELLFF.KKLDGP.HQEVL.ILQENLD.EVLDDEILAELA.PTE.AQ
Retrocopy AVPYVWPADEDTEESEHLTQAEWWELLFFFKKLDGPNHQEVLHILQENLDREVLDDEILAELAMPTEVAQ

Parental  DLLLALPQRLDDSALRDLLNCRVYRKYG-PEALAGQLAHPSLLEAWAQPQESADAARVEAKEAPTQGSNT
          DLLLALPQRLD..ALRD.LNCRVYRKYG.PEALAGQ.AHPSLLEAWAQPQESADAARVEAKEAPTQGSNT
Retrocopy DLLLALPQRLDNRALRDVLNCRVYRKYG<PEALAGQPAHPSLLEAWAQPQESADAARVEAKEAPTQGSNT

Parental  PLQRLAEGFGPAGKIFLDLEEAFRSEG-PQQGEAKPLLLQLQRQPQPFLVLMRSLDTPAANKPLHLAVLR
          .LQ.LAEGFGPAGK.FLDLE.AF.SEG.P.QGEAKPLLLQLQRQPQPFLVLMRSL.TPAANKPLHLAVLR
Retrocopy LLQHLAEGFGPAGKVFLDLEGAFHSEG>PRQGEAKPLLLQLQRQPQPFLVLMRSLNTPAANKPLHLAVLR

Parental  ILMQLVDFPEALLLPWHEAMDACMACLRSPNTDREVLQELILFLHRLASVSRDYAVVLNQLGARDAISKA
          ILMQLVDFPEALLLPWHEAMD.CMACL.SPNTDREVLQELILFLHRLAS.SRDYAVVLNQLGARDAISKA
Retrocopy ILMQLVDFPEALLLPWHEAMDTCMACLQSPNTDREVLQELILFLHRLASISRDYAVVLNQLGARDAISKA

Parental  LEKHLGKLELAQELRDMVFKCEKHAHLYRKLTTNILGGCIQMVLGQIEDHRRTHRPINIPFFDVFLRYLC
          LEKHLG.LELAQELRDMVFKCEKHAHLYRKLTTNILGGCIQMVLGQIEDHRRTH.PINIPFF.VFLRYLC
Retrocopy LEKHLGELELAQELRDMVFKCEKHAHLYRKLTTNILGGCIQMVLGQIEDHRRTHHPINIPFFNVFLRYLC

Parental  QGSSMEVKEDKCWEKVEVSSNPHRASKLTDRNPKTYWESNGSAGSHRITLHMQQGILIRQLALLVASEDL
          .GSSMEVKEDKCWEKVEV.SN.H.ASKLTDRNPKTYWESNGSAGSH.ITLHMQQGILIRQLALLVASEDL
Retrocopy *GSSMEVKEDKCWEKVEVLSNLHWASKLTDRNPKTYWESNGSAGSHHITLHMQQGILIRQLALLVASEDL

Parental  SYMPARVVVFGGDSATSLNTELNSVNVMPSASRVVLLENLSRVWPVIQIRIKRCQQGGIDTRIRGLEVLG
          SYMPARVVVFGGDS.TSLNTELNSVNVMPSAS.VVLLENLSR.WP.IQIRIKRCQQGGIDT.I.GLEVLG
Retrocopy SYMPARVVVFGGDSTTSLNTELNSVNVMPSASQVVLLENLSRIWPIIQIRIKRCQQGGIDTCIWGLEVLG

Parental  PKPTFWPVFREQLCRHTRLFYMVRAQAWSQDIAEDRRGLLHLSSRLNGALRHEQNFASCFLPDEEAAQAL
          PKPTFWPVFREQLCRHTRLFYMV.AQAWSQDI.ED.RGLLHLSSRLNGALRHEQNFAS.FLPDEEAAQAL
Retrocopy PKPTFWPVFREQLCRHTRLFYMVQAQAWSQDIVEDHRGLLHLSSRLNGALRHEQNFASHFLPDEEAAQAL

Parental  GKTCWEALVSPLVQNITCPDEEGVSPLGWLLDQYLECREAAHNPQSRAAAFSSRVRRLTHLLVHVEPCEA
          GKT.WEALVSPLVQNITCPDEEGVSPLGWLLDQYLEC.E.AHNPQS.AAAFSS.V.R.THLLVH.EPCEA
Retrocopy GKTYWEALVSPLVQNITCPDEEGVSPLGWLLDQYLECQEPAHNPQSHAAAFSSWVCRITHLLVHMEPCEA

Parental  PPSVAATPRPKGRNRSHDWSSLATRGLPSSIMRNLTRCWRAVVEEQVHSFLTSRWRDDDFVPRYCEHFSN
          P..VAA.PRPKGRNRSHDWSSLATRGLPSSIMRNLT.CWRAVVEEQVHSFLTS.W.DDDFVP.YCEHF.N
Retrocopy PHLVAASPRPKGRNRSHDWSSLATRGLPSSIMRNLTHCWRAVVEEQVHSFLTSCWQDDDFVPHYCEHFGN

Parental  LQKASSELFGPRAAFLLALQNGCAGALLKLPFLRAAHVSEQFARHIDQRIQGSRIGGARGMEMLAQLQRC
          LQKASSELFGPRAAFLLALQNGCAGALLKLPFLRA.HVSEQFA.HIDQRIQGS.IGGARGMEMLAQLQ.C
Retrocopy LQKASSELFGPRAAFLLALQNGCAGALLKLPFLRAGHVSEQFAQHIDQRIQGSWIGGARGMEMLAQLQLC

Parental  LETVLIFSGLEIATTFEHYYQHYMADRLLGVGSSWLEGAVLEQIGPCFPTRLPQQMLRSLSTSEELQRQF
          LET.LIFSGLEIATTF.HYYQHYMADRLLGVGSSW.EGAVLEQIGPCFP.RLPQQML.SLSTSEELQ.Q.
Retrocopy LETILIFSGLEIATTFKHYYQHYMADRLLGVGSSWREGAVLEQIGPCFPNRLPQQMLQSLSTSEELQHQL

Parental  HVYQLQRLDQELLKLEDTEKKIQVSRDASASGRGHERGTGEEAELEAGAVAAAAAAGVAGEEEEE
          HVYQLQRLDQELLKLEDTEKKIQVSRD..ASGRGHERGTGEEAELEA.A.AAAA.A.VAGEEE.E
Retrocopy HVYQLQRLDQELLKLEDTEKKIQVSRD--ASGRGHERGTGEEAELEAAALAAAATASVAGEEE*E

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	14.13 RPM
ERP005899_muscle	0.42 RPM	111.17 RPM
SRP017611_brain	0.18 RPM	140.65 RPM
SRP017611_kidney	0.12 RPM	134.67 RPM
SRP017611_liver	0.00 RPM	50.21 RPM
SRP030211_testis	0.27 RPM	53.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1639 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012749	1 retrocopy	retro_btau_1639 ,