RetrogeneDB ID: retro_btau_1177

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:24104736..24105601(+)
• 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_1177
CATTGGGCCCAGGAACTGCTAATGAACACTGAACATACAGGGCAGTGGTGGTTCAAGAAATGTTGCAAATCTTGCAAATG
TCACAAGAAAGATTCAAGTGACAGCCTTGAAGAGGAGGAGCACGGTGGCTGGCCATCGGAATTTGACAATGACCAACTGA
GAGGATCACTGAAGCTGATCCTCTTACAACTACATGAAAAGTTGCCAAAGAACTCAGTGTTAACCATTCTATGGTTGTTC
AGTATTTGAAGCAAATTGGAAAGGTGAAAAAGTTCGGTAAGTTGGTGCCTCATGAGCAGACTGCAAATAAAAAAAAAATT
ATTGTTTTGAAGTGTCATCTTCTCTTATTCTAGGCAACAACAACAAACCATTTTTTGATCAGATTTTGACATTTAATGAA
AAGTGAATTTCATACAACAACCAAGTCAGTGGCTGAACCAAGAAGAAGCTCCAAAGCACTTTCCAAAGCCAAGCTTGCAT
GAGAAAAAGGTCATGGTCACTCTTTGGTGGTCTGCTGCTGGGTCTCATCCACTACAGCTTTCTGAATCCGACTGAAACCA
TTACATCTGAGAAGTATGCTCAGCAAATCAGTGAGGTACACTGACAACTGCAAAGCCTGCAGCTGGCACCAATCAACAGA
AAGGGTCCAATTCTTCTCCATGACAGCTCCTGATGACATGTCACACAATCAACGCTTCAAAAGTTGAACAAATTGGGCTA
AAAAGTTTTGCATCATCCACCATATTCACTTGACCTTTCGCCAAGCAACTGCTACTTCCTCCAGTATCTCGACAACATTT
TTCAGGGAAAACACTTCCACAACCAGCAGGACACAGAAAATGCTTTCCGAGACTGCATCAAATCC

Alignment

ORF - retro_btau_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.88 %
• Parental protein coverage: 92.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HKAMETICNINNAFSPGTANECTVQWCFKKFCKRDESLEEEHGGLPSEADNDQLSRSSKLIILQVQEKLP
          H.A.E...N............C....C.KK....D...EEEHGG.PSE.DNDQL..S.KLI.LQ..EKLP
Retrocopy HWAQELLMNTEHTGQWWFKKCCKSCKCHKKDSS-DSLEEEEHGGWPSEFDNDQLRGSLKLILLQLHEKLP

Parental  -QELNVNHSMVIWHLKQIGKVKKLSKRALHA-AACFMSQKQIKMMSSLSLCNN-SEPF-LNRLWHVIKSE
          ..EL.VNHSMV...LKQIGKVKK..K...H..A.C..........SS.....N...PF.L.R..H..KSE
Retrocopy <KELSVNHSMVVQYLKQIGKVKKFGKLVPHE<ADCKXXXXYCFEVSSSLILGNNNKPF>LIRF*HLMKSE

Parental  LYTTTGN--NQRRSSKALPKAKLT-PKNVVVTVWWSAA-GLTHYNFLNPSETITSEKNGQQISEVNQKLQ
          ..TTT......RRSSKAL.KAKL...K.V.VT.WWSAA.GL.HY.FLNP.ETITSEK..QQISEV...LQ
Retrocopy FHTTTKSVAEPRRSSKALSKAKLA>EKKVMVTLWWSAA>GLIHYSFLNPTETITSEKYAQQISEVH*QLQ

Parental  SLQAVLLNRKGPVLFHDNTQLHVS-ANASKVSKLGYKVLPHPPYSPEDLWPIEYHFFKHLHN-FQGKCFH
          SLQ....NRKGP.L.HD....HV......K..KLG.KVL.HPPYS..DL.P....F...L.N.FQGK.FH
Retrocopy SLQLAPINRKGPILLHDSS**HVTQSTLQKLNKLG*KVLHHPPYS-LDLSPSNCYFLQYLDNIFQGKHFH

Parental  KQQEAENAFQKFIES
          .QQ..ENAF...I.S
Retrocopy NQQDTENAFRDCIKS

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	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.00 RPM	0.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1177 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1177 has 0 orthologous retrocopies within eutheria group .

---

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,