RetrogeneDB ID: retro_btau_518

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:66538434..66538936(+)
• Located in intron of: ENSBTAG00000019621

Retrocopy information

• Ensembl ID: ENSBTAG00000046344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C6ORF108
• Ensembl ID: ENSBTAG00000019913
• Aliases: None
• Description: None

Sequence

>retro_btau_518
GCGGCGGCTGGAATCCTGGTGCGCGGGGAGCCGGGTCTTCTCTCCCTGTACTTCTGCGGGAGTATCCGCGGCGGACGAGA
GGACCGGGAACTGTACGTGCTCATCGTGTCTCGCCTCCGGAGCTTCGGGGTGGTGCTCACCGAGCATGTGGCGGCCGCCG
AGCTGGACAAGAGCAGGGAAGAGGCTGCTGGAGGCGACAAGTTCATCCATGATCGGGACCTGGCCTGGCTGCAGCAGGCA
GATGTGGTCGTGGCAGAAGTGACCCAGCCCTCTCTGGGGGTAGGCTATGAGCTGGGCCGGGCTGTGGCCCTCCACAAACC
AGTCCTGTGCCTGTTTCGCCCAAAGTCTGGCCGAGTGCTCTCAGCCATGATCCAGGGAGCAGCCGATGGCTCCAGGTTCC
AGGTGTGGGACTACGGAGGAAGCAGAGGTGGAGGCCCTGCTAGATCGGTACTTTGAGGCATATCCTCCTGAGCAGGTGGC
TGCCTCTCCTGACCCAACTGCT

Alignment

ORF - retro_btau_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAGTVDPGRLSLYFCGSIRGGREDRELYVRIVSRLRRFGVVLTEHVAAAEVDESATGEEAAGGDKL
          AAA.......PG.LSLYFCGSIRGGREDRELYV.IVSRLR.FGVVLTEHVAAAE.D.S...EEAAGGDK.
Retrocopy AAAGILVRGEPGLLSLYFCGSIRGGREDRELYVLIVSRLRSFGVVLTEHVAAAELDKSR--EEAAGGDKF

Parental  IHDRDLAWLQQADVVVAEVTQPSLGVGYELGRAVALHKPVLCLFRPKSGRVLSAMIRGAANGSRFQVWDY
          IHDRDLAWLQQADVVVAEVTQPSLGVGYELGRAVALHKPVLCLFRPKSGRVLSAMI.GAA.GSRFQVWDY
Retrocopy IHDRDLAWLQQADVVVAEVTQPSLGVGYELGRAVALHKPVLCLFRPKSGRVLSAMIQGAADGSRFQVWDY

Parental  -EEAEVEALLDRYFEAYPPEQVAASPDPTA
          .EEAEVEALLDRYFEAYPPEQVAASPDPTA
Retrocopy >EEAEVEALLDRYFEAYPPEQVAASPDPTA

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	3.68 RPM
ERP005899_muscle	0.16 RPM	31.52 RPM
SRP017611_brain	0.05 RPM	5.16 RPM
SRP017611_kidney	0.41 RPM	12.80 RPM
SRP017611_liver	0.00 RPM	8.08 RPM
SRP030211_testis	0.03 RPM	5.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_518 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_518 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518 ,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,