RetrogeneDB ID: retro_btau_1096

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:12371721..12372670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000002851
• Aliases: None
• Description: None

Sequence

>retro_btau_1096
ACTACAGAAATGACATTAGACAAAAAGCCAATTTGAGTGATTTTTTAATTTCAGTTCAAAACGGGTCGTAAAAGAGCAGA
GACAACTTGCAGCATCAGCAATGCATTTGGCCCAGGAATTGCTAATGAACGACAGTGCAGTGGTAGTTTCAGAAGTTTTG
TAAAGGAGACAAGAGCCTTGGAGATGTGGAGCACAGTGGTCAGCCATCAGAAGCTGACAAAGACCAACTGAGAGCAATCA
TCAAAGCTGATCCTCCTACAACTACACAAGAAGTTGCCAGAGAACTCAACATCGACCATTCTACGGTCATTCAGCATTTG
AAGCAAATTGGAAAGGTGACAAAGCTCGATTAAGCAGGTGCCTCATGAGACAACAGGGAATTTAAAAAATTGTTGTTTTG
AAATATCATCTTCTTTTATTCTATGCAACAACAATGAGCCATTTCTCAATGGGAATGTGACATTTAACAAAAAGTTGATT
TTATATGACAACCAGCCGTGACCAGCTCAGTGGTAAGACTGAGAAGAAGCTCCCAAGCGCTTCCCAAAGTCAAACTTGCA
CCAAAAAATAAGTCATGGTCACTGTTTGGTTGTCTGCTGCTGGTCTTATCCACTACACCTTTCTGAATCCCAGCAAAACC
ATTTCATCTGAGAAGTATGCTCAGCAAATCGATGAGATGCACTGAAAACCGCAAAGCCTGCAGCCAGCATTGGTCAACAG
AAAGGGCTCAATTCTTCTCCACAACAATGCCCGATTGCACATCACACAGCCAACGCTTCAAAAGCTGAACGAACTGGGCT
ACAAAGTTTTGCCTCATCTGCCATACTCACCTGACCTCTCTCTCACCCACCAACTACAACTCCTTCAAGCATCTCACAAC
TGTTTGCAGGGAAAATGCGTCCATAACCCGCAGGAGGCAGAAAATGCTTTCCAAGCGTTCATGAAATCC

Alignment

ORF - retro_btau_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TREMMLDKKQIRMIFLFKFKLGHKAMETICNINNAFSPGTANE-CTVQWCFKKFCKRDESLEE-EHGGLP
          T.EM.LDKK.I..IF.F.FK.G.K..ET.C.I.NAF.PG.ANE..TVQW.F.KFCK.D.SL...EH.G.P
Retrocopy TTEMTLDKKPI*VIF*FQFKTGRKRAETTCSISNAFGPGIANE<TTVQW*FQKFCKGDKSLGDVEHSGQP

Parental  SEADNDQL-SRSSKLIILQVQEKLPQ-ELNVNHSMVIWHLKQIGKVKKLS-KRALHAAACFMSQKQIKMM
          SEAD.DQL...SSKLI.LQ...KLP..ELN..HS.VI.HLKQIGKV.KL..K...H..............
Retrocopy SEADKDQL>EQSSKLILLQLHKKLPE<ELNIDHSTVIQHLKQIGKVTKLD>KQVPHETTGNLKNCCFEIS

Parental  SSLSLCNNSEPFLN-RLWHVIKSELYTTTGNNQ--RRSSKALPKAK----LTPKNVVVTVWWSAAGLTHY
          SS..LCNN.EPFLN....H..KS..Y.TT...Q......K.LP.A......T.K.V.VTVW.SAAGL.HY
Retrocopy SSFILCNNNEPFLN>GM*HLTKS*FYMTTSRDQLSGKTEKKLPSASQSQTCTKK*VMVTVWLSAAGLIHY

Parental  NFLNPSETITSEKNGQQISEVNQKLQSLQAVLLNRKGPVLFHDNTQLHVS-ANASKVSKLGYKVLPHPPY
          .FLNPS.TI.SEK..QQI.E...K.QSLQ..L.NRKG..L.H.N..LH.......K...LGYKVLPH.PY
Retrocopy TFLNPSKTISSEKYAQQIDEMH*KPQSLQPALVNRKGSILLHNNARLHITQPTLQKLNELGYKVLPHLPY

Parental  SPE-DLWPIEYHFFKHL-HN-FQGKCFHKQQEAENAFQKFIES
          SP...L.P..Y..FKHL.HN..QGKC.H..QEAENAFQ.F..S
Retrocopy SPD>SLSPTNYNSFKHL<HNCLQGKCVHNPQEAENAFQAFMKS

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	0.00 RPM	0.00 RPM
SRP017611_brain	0.23 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.30 RPM	0.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1096 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1096 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002851	9 retrocopies	retro_btau_1096 , retro_btau_1110, retro_btau_1177, retro_btau_1204, retro_btau_1363, retro_btau_1525, retro_btau_392, retro_btau_831, retro_btau_846,