RetrogeneDB ID: retro_btau_1337

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:2819845..2820238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBP
• Ensembl ID: ENSBTAG00000009287
• Aliases: None
• Description: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase [Source:RefSeq peptide;Acc:NP_001029672]

Sequence

>retro_btau_1337
CTCTGGAAAGAGTATGCCAAGGGAGGCAGTCAATACGTCCTGAATGATAACTTCATGATATGCATGGAGACCATCATGGC
TTACCTTTAGGGGATCACTCAGCCTGTGGATAGTGATCGCTTTTCTCCACCAGCAACCCCTTCACTTTATCCTACAGCTT
GTGATCTCTGTGAGTCAGGTATATGGAGATGTGCTCTATTTCCTGATGGGGTACCGTGATGGATTCCAGCACAGGGAGCT
GGGACACCCACTCGACTTCTGGTTTTACTTTGTCTTCCTGAACGCCCTGTGGCTGGCGCTGCCTGGACTCCTCATACTGG
CTTCCATAAAGCAACTTGCTCATGCCCAGAGCATACTGGTGCCAAAGCCCCCAAAGCTAGGAGCAAGCAGAAC

Alignment

ORF - retro_btau_1337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.7 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LWKEYAKGDSRYILNDNFMICMETVTAYL-WGPLSLWVVIAFLRHQPLRFVLQLVVSMGQVYGDVLYFLT
          LWKEYAKG.S.Y.LNDNFMICMET..AYL..G.LSLW.VIAFL..QPL.F.LQLV.S..QVYGDVLYFL.
Retrocopy LWKEYAKGGSQYVLNDNFMICMETIMAYL>RGSLSLWIVIAFLHQQPLHFILQLVISVSQVYGDVLYFLM

Parental  EYRDGFQHGELGHPLYFWFYFVFLNSLWLVVPGLLILDSIKQLAHAQSIL-DAKAPKAKSKQN
          .YRDGFQH.ELGHPL.FWFYFVFLN.LWL..PGLLIL.SIKQLAHAQSIL..AKAPKA.SKQN
Retrocopy GYRDGFQHRELGHPLDFWFYFVFLNALWLALPGLLILASIKQLAHAQSIL<GAKAPKARSKQN

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	90.48 RPM
ERP005899_muscle	0.00 RPM	37.27 RPM
SRP017611_brain	0.00 RPM	7.31 RPM
SRP017611_kidney	0.00 RPM	22.40 RPM
SRP017611_liver	0.00 RPM	67.05 RPM
SRP030211_testis	0.00 RPM	2.04 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1337 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009287	1 retrocopy	retro_btau_1337 ,
Dipodomys ordii	ENSDORG00000013766	1 retrocopy	retro_dord_32,
Otolemur garnettii	ENSOGAG00000016187	3 retrocopies	retro_ogar_1190, retro_ogar_1191, retro_ogar_1942,
Procavia capensis	ENSPCAG00000009202	1 retrocopy	retro_pcap_218,