RetrogeneDB ID: retro_btau_898

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:7900179..7901888(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNPO2L
• Ensembl ID: ENSBTAG00000021132
• Aliases: None
• Description: None

Sequence

>retro_btau_898
AAAATCCGAAGATGGAGCCGGGCAGGCAGAGCAGGACTCCAAGACAGGGATCAGCTTTTGGCCATCACTGGGGTCTCCTG
CACCAGCCTCTCTCATGCCAGTGCCACAAGCCTCATCAATGTCTCAGGGAATCGGCCTGTCCTCGCTGTGCAGCGGGTAG
AGGACGAGGGACCTGTGCGATCGCCATCCCCGGGTGAGCTTCAGGCACTGTCACCAGTGTCTCCACTGAGTCCTGAGCCC
CCAGGAGCTCCGGTTCCCCAGCCTCTCCAGCCCAGGTGTCTCCTCTCGCCCCCTGACAGTGAGGCTTACTAAGGACAGAC
AGTGATGCTGACAGCCCAGCCACCCAGGAAAAGCCCCGCCGACCCCACCACTGAGGCTCCACAAGGCCCACCCCTCCAGG
AGCCCTACCAGATGAGGTCTACCTGTCTGACAGCCCTGCAGAGCCGGCACCTGCTGTCCTTGGCCCTCCCAGCCAGGGTG
ACAGTCGTGTGAGCTCCCCATCTTGGGAGGATAGGACAACTCTTCAGCCACCCCCTGATGAGGCCCTGCTGTTGCCCCAT
GGCCCCCTCCGGCCTGGCCCTCATCTCATCCCTATGGCGGGGCCTGTTCCCCACCCAGTGGCAGAAGATCTTACCACCAC
CTATACCCAGAAGGCCAAACAAGCCAAGCTACAAAGGGCAGAGAGCCTCCAAGAGCGGAGTGTGAAGGAGGCCAAGACCA
AATGCCGGACGATTGCATCCTGCTCACCGCAGCCCCTAACCCCCACTCCAAGGGGGTACTGATGTTTAAGAAACGTCAGC
AGAGAGCCAAGAAATACACCCTAGTGAGCTTTGGGGCTGCCGTGGGGACCGGCGCTGAGGAGGAGGACGGCTTGCCTCCA
ACCAGTGAGTCCCAGCTGGAGGAAGAGGCTTTCTCCGAAGCCCGCAGCCTCAACAACCAGTCCGACTGGGAGAGCCCCTA
CCTAGACATGGAGCTAGCCAGACCGAGCTCAGGCACAGCAGAGGGCCGGGGGCTGGGAGGGCAGCCGAGTGAGGCCTCCA
GGCGAGGGGCCCAACTCTTTGAACAGCAGTGCCAGCGCGCAGCCTCCATCACCCAGCAGCTGGCCCAGGAAGGTCCAGCG
GCCACGCTCAAGGGGCAGGGCCTGCAGTCTCCACCTCGGCCACAAAACGCTCCGCCAGAGGCGGCTCTACTCCCATCCAG
CCCTTTGCCAGCCCCTGTGGTCAGCCCCAGACCTTTCCTCCCCAGCTGTGGAACCTCTACCTCAGCTCCAAGCATCTTTA
ACCATTCAGCTAGCACTCCCGGCTTACAAGGGCAGCGGTCAGGTACCACCTTGCTTATTTTCTGGCCCCTAGCTCCCAAG
AGGGCAAATGAGAGCCTGGGAGGCCTCAGCACCGCCCCACCGCCTTTCCTATCTCCTCCGCAGGGTACCTTTCCTGTGCC
CAGCTTCACTTAAGGGGTTCCAAGCCATGTGCCAGTCCCCACTTCCCCCAGCACCCCACGCTCCCCCGGCCCCATGACAG
CCACCAGCTCCCTATACATCCCAGCCCCTAATCATCCTGTTACACCAGGCGGAGCCCAGAGCCTCCGGCCCCCGCTAGCG
GAGCCGCCATGACCTCCACCACTTCTATCTTCCTGTCATCGCCTCTGCGACCTGCTGCGTGCCCAGAAGCGCCTGCCCCT
CTAGCTCTGCGGCCCCTGAGCCCCACAGC

Alignment

ORF - retro_btau_898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.6 %
• Parental protein coverage: 94.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KIRRRSQAGRAGLRERDQLLAINGVSCTSLSHASAMGLIDASGNQLVLTVRRVEDEGPVRSPSPGELQAR
          KIRR.S.AGRAGL..RDQLLAI.GVSCTSLSHASA..LI..SGN..VL.V.RVEDEGPVRSPSPGELQA.
Retrocopy KIRRWSRAGRAGLQDRDQLLAITGVSCTSLSHASATSLINVSGNRPVLAVQRVEDEGPVRSPSPGELQAL

Parental  SPLSPLSPEPPGAPVPQPLQPGSLLSPPDSEAYYGETDSDADGPATQEKPRRPRRRGP-TRPTPPGAPPD
          SP.SPLSPEPPGAPVPQPLQP..LLSPPDSEAY.G.T......P.....P..P....P.TRPTPPGA.PD
Retrocopy SPVSPLSPEPPGAPVPQPLQPRCLLSPPDSEAY*GQTVMLTAQP-PRKSPADPTTEAP<TRPTPPGALPD

Parental  EVYLSDSPAEPAPAVLGPPSQGDSRVSSPSWEDGTTLQPPPAEALLLPHGPLRPGPNLIPMVGPVPHPVA
          EVYLSDSPAEPAPAVLGPPSQGDSRVSSPSWED.TTLQPPP.EALLLPHGPLRPGP.LIPM.GPVPHPVA
Retrocopy EVYLSDSPAEPAPAVLGPPSQGDSRVSSPSWEDRTTLQPPPDEALLLPHGPLRPGPHLIPMAGPVPHPVA

Parental  EDLTTTYTQKAKQAKLQRAESLQERSVKEAKTKCRTIAA-LLTAAPNPHSKGVLMFKKRRQRAKKYTLVS
          EDLTTTYTQKAKQAKLQRAESLQERSVKEAKTKCRTIA..LLTAAPNPHSKGVLMFKKR.QRAKKYTLVS
Retrocopy EDLTTTYTQKAKQAKLQRAESLQERSVKEAKTKCRTIAS<LLTAAPNPHSKGVLMFKKRQQRAKKYTLVS

Parental  FGAAAGTGAEEEDGLPPTSESELDEEAFSDARSLTNQSDWDSPYLDMELARPSSGTAEGRGL----SEAS
          FGAA.GTGAEEEDGLPPTSES.L.EEAFS.ARSL.NQSDW.SPYLDMELARPSSGTAEGRGL....SEAS
Retrocopy FGAAVGTGAEEEDGLPPTSESQLEEEAFSEARSLNNQSDWESPYLDMELARPSSGTAEGRGLGGQPSEAS

Parental  GRGAQLFEQQRQRTASITQQPAQEVPVATLNGQGLQSPPRPQSAPPEAALLPSSPSPAPVASPRPFLPGC
          .RGAQLFEQQ.QR.ASITQQ.AQE.P.ATL.GQGLQSPPRPQ.APPEAALLPSSP.PAPV.SPRPFLP.C
Retrocopy RRGAQLFEQQCQRAASITQQLAQEGPAATLKGQGLQSPPRPQNAPPEAALLPSSPLPAPVVSPRPFLPSC

Parental  GTSTSAPSIFNRSARPFTPGLQGQRSGTTSVIFRPLAPKRANESLGGLSPAPPPFLSPPQGTTPVPSLTS
          GTSTSAPSIFN.SA...TPGLQGQRSGTT..IF.PLAPKRANESLGGLS.APPPFLSPPQGT.PVPS.T.
Retrocopy GTSTSAPSIFNHSAS--TPGLQGQRSGTTLLIFWPLAPKRANESLGGLSTAPPPFLSPPQGTFPVPSFT*

Parental  GVPSHVPVPASPSTPRPTGPVTATSSLYIPAPNRPVTPGGA-PEAPAPASGAAMTSTASIFLSSPLRPAA
          GVPSHVPVP.SPSTPR..GP.TATSSLYIPAPN.PVTPGGA.PE.PAPASGAAMTST.SIFLSSPLRPAA
Retrocopy GVPSHVPVPTSPSTPRSPGPMTATSSLYIPAPNHPVTPGGA<PEPPAPASGAAMTSTTSIFLSSPLRPAA

Parental  RPEAPA-PSS-AAPEPPS
          .PEAPA.PSS.AAPEP.S
Retrocopy CPEAPA<PSSSAAPEPHS

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	0.00 RPM
ERP005899_muscle	0.05 RPM	0.05 RPM
SRP017611_brain	0.00 RPM	0.14 RPM
SRP017611_kidney	0.00 RPM	0.47 RPM
SRP017611_liver	0.00 RPM	0.15 RPM
SRP030211_testis	0.00 RPM	1.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_898 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_898 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	ENSBTAG00000021132	1 retrocopy	retro_btau_898 ,