RetrogeneDB ID: retro_btau_1525

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:24039601..24040527(+)
• Located in intron of: ENSBTAG00000025443

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_1525
AGGGAAATGATGCTAGACAAAAAGCAATTATGAGGGAGTTTCTTATTTCAGTTCAAAATAAGTCCTAAAGCAGTGGCGAG
AACTCACAACATCAACAACTCATTTCGCCCAGGAATTGCTAATGAACGTATAGCGCAGTGGTGGTTCAAGAAGTTTTGCA
AAGGAGACAATTGCCTTGAAGATGAGGAGCATAGTGGCCAACCATCAGAAGTTGACAATGACCAACTGATAGGATCATCA
AAACTGATCCTCTTAAAACTACATGAGAAGTTGCTGAAGAACTCAGCATCGATCATACTATGGTCATTTGGCATTTGAGG
CAAATTGGAAAGGTGAAAAAAGCTCGATAAATCGTTCCCTCATGAGCTGACGGCAAATCAAAAAAATTATCAATTTGAAG
TGTTGTCTTCTCTAATTGTACACAACAACGAACCATCTCTTGATCAGATTGTGACGTGTGATGAAAAGTAGATTTTATAT
GATGACCAGCTCAGTGGTTGGACCAAGAGGAAGCTTCAAGCACTTCCCAGAGTCCAGCTTACACCAGAAACAGGTCATGG
TCACTGTTTGGTGGTCTGTTGCTGGTCTGATCCATTACAGCTTTATGAATCCAAGTGAACCCACTATATCTGAGAAGTAT
GCTCAGCAGATCAATGAGATTCACTAAAAACCGCAGTGCCTGTAGCCAGCTTTGGTCAACAGAATGGACTCAATTCTTCT
CCATGACAACGCCCACCCCAGATTGCACAACCAACACTTGAAAATTTAAATGAACTGGACTACGAAGTGTTGCCTCATCT
GCCATTTCACCTGACTTTTCACCAACTGACAACCACTTCTTCAAGCATCTTGACAACTTTTTGCAGAGAAAATGCTTCCA
CAACCAGCAGGAGGCAGAAAATGCTTTCCAAGTGTTCGTTGAATCC

Alignment

ORF - retro_btau_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.23 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REMMLDKKQIRMIFLFKFKLGHKAMETICNINNAFSPGTANECTVQWCFKKFCKRDESLE-EEHGGLPSE
          REMMLDKKQ....FLF.FK...KA.....NINN.F.PG.ANE...QW.FKKFCK.D..LE.EEH.G.PSE
Retrocopy REMMLDKKQL*GSFLFQFKISPKAVARTHNINNSFRPGIANERIAQWWFKKFCKGDNCLEDEEHSGQPSE

Parental  ADNDQLSRSSKLIILQVQEKL-PQELNVNHSMVIWHLKQIGKV-KKLSKRALHAAACFMSQKQIKMMSSL
          .DNDQL..SSKLI.L...EKL...EL...H.MVIWHL.QIGKV.KKL.K...H.........Q....SSL
Retrocopy VDNDQLIGSSKLILLKLHEKL<AEELSIDHTMVIWHLRQIGKV>KKLDKSFPHELTANQKNYQFEVLSSL

Parental  SLCNNSEPFLN-RLWHVIKSELYTTTGN--NQRRSSKALPKAKLTPKNVVVTVWWSAAGLTHYNFLNPSE
          ....N.EP.L..RL..V.KS..Y..T......R.S.K..P...L..K.V.VTVWWS.AGL.HY.F.NPSE
Retrocopy -IVHNNEPSLD>RL*RVMKSRFYMMTSSVVGPRGSFKHFPESSLHQKQVMVTVWWSVAGLIHYSFMNPSE

Parental  TITSEKNGQQISEVNQKLQSLQAVLLNRKGPVLFHDNTQLHV-SANASKVSKLGYKVLPHPPYSPEDLWP
          ...SEK..QQI.E...K.Q.L...L.NR....L.HDN........N..K....G.........SP.D..P
Retrocopy PTISEKYAQQINEIH*KPQCL*PALVNRMDSILLHDNAHPRL>TTNT*KFK*TGLRSVASSAISP-DFSP

Parental  IEYHFFKHLHNF-QGKCFHKQQEAENAFQKFIES
          ...HFFKHL.NF.Q.KCFH.QQEAENAFQ.F.ES
Retrocopy TDNHFFKHLDNFLQRKCFHNQQEAENAFQVFVES

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	0.26 RPM	0.00 RPM
SRP017611_brain	0.37 RPM	0.00 RPM
SRP017611_kidney	0.24 RPM	0.00 RPM
SRP017611_liver	0.08 RPM	0.00 RPM
SRP030211_testis	0.10 RPM	0.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1525 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1525 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,