RetrogeneDB ID: retro_btau_618

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:33041007..33041367(+)
• Located in intron of: ENSBTAG00000024555

Retrocopy information

• Ensembl ID: ENSBTAG00000047437
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BCL7C
• Ensembl ID: ENSBTAG00000008412
• Aliases: None
• Description: None

Sequence

>retro_btau_618
GAGGAGCACCGGAGGGCAGGTGGAGGGGCGGAGAGATCCCGAGGCTGGGAGCGGAGGGGCAGGGGTGCCAGTCCCTGAGG
GGGTGGCCCTCTCATCCTGCTGGATCTCAATGATGAGAACAGTAACCAGAGTTACTCAGCCTTCCATTCAGAAGGCTCCC
TGCAGAAGAGCACGGGGCCCAGCCCTGGGGGCACCCCCCAGCCCAGCCGTCCTGTGTCACCTGCTGGACCACCAGAAGGG
GTTCCAGAGGATGCTCAGCCCCCACAGGTGGACCAGGAGAGAGATCCTGGGGGCATACCTGCGGGCAGCATGGATGAACC
CCCCATGTTGGCCAAGGAGGAGCCTGTTCCAGAATTGCTG

Alignment

ORF - retro_btau_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 72.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QERRRAGGGAERSRGRERRGRGASPRGGGPLILLDLNDENSNQS---FHSEGSLQKGTEPSPGGTPQPSR
          .E.RRAGGGAERSRG.ERRGRGASP.GGGPLILLDLNDENSNQS...FHSEGSLQK.T.PSPGGTPQPSR
Retrocopy EEHRRAGGGAERSRGWERRGRGASP*GGGPLILLDLNDENSNQSYSAFHSEGSLQKSTGPSPGGTPQPSR

Parental  PVSPAGPPEGVPEDAQPPQLGQERDPGSIPGILGMSPPHVTYSVPGPVLM
          PVSPAGPPEGVPEDAQPPQ..QERDPG.IP......PP......P.P.L.
Retrocopy PVSPAGPPEGVPEDAQPPQVDQERDPGGIPAGSMDEPPMLAKEEPVPELL

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	0.14 RPM	1.08 RPM
ERP005899_muscle	1.11 RPM	8.08 RPM
SRP017611_brain	0.59 RPM	1.78 RPM
SRP017611_kidney	1.19 RPM	7.17 RPM
SRP017611_liver	0.38 RPM	3.25 RPM
SRP030211_testis	1.73 RPM	32.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_618 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_618 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618 ,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613, retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,