RetrogeneDB ID: retro_btau_1285

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:78756420..78757197(-)
• Located in intron of: ENSBTAG00000005442

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSBTAG00000022731
• Aliases: None
• Description: Translocon-associated protein subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:A6QLP7]

Sequence

>retro_btau_1285
ATGAGGTCCCTCCACCGCCTGCTGCTGCTTCTGCTGGTGCTCCCCACCACCCTCCTGCTCCGAGGCGGCCCAGGAGGCTC
ATTGGCAGTGGCTCAGGATCTTACAGAAGATGAAGAAACAGTGGAAGATTCTATAATTGACGATGAAGACGATGAAGCAG
AGGTGGAAGAAGATGAACCGACAGATTTGGCTGAAGATAAAGAGGAAGATGATGTATCAGGTGAACCTGAAGCTTCACCA
AGTGCAGATACAACCATCCTGTTTGTGAAAGGAGAAGATTTTCCAGCAAATAACATTGTGAAGTTCCTGGTAGGCTTTAC
AAACAAGGGTACAGAAGATTTTATCGTCGAGTCTCTCGACGCCTCATTCCGTTACCCTCAGAATTACTAGTTTTATATTC
AGAATTTCACTGCTCTTCCTCTGAACACGGTCGTGCCGCCCCAGAGATAGGCAACCTTTGAGTACTCCTTCATCCCCGCA
GAGCCCATGGGCGGCCGGCCCTTCGGTCTGGTCATCAACCTGAACTACAAGGATTTGAACGGCAATGTTTTCCAAGATGC
TGTCTTCAATCAAACAGTTACAATTATCGAGAGAGAAGATGGGTTAGATGGAGAAACCATATTTATGTACATGTTCCCGG
CTGGTCTCGGGCAGCTGGTTGTCGTCGGCCTTCATCAGCTCCTGGAATCTAGAAAGCGCAAGAGGCCCATTCAGAAGATA
GAGATGGGAACCTCAAGTCAAAACGACGTTGACATGAGCTGAATTCCTCAGGAAACT

Alignment

ORF - retro_btau_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.62 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSLRRLLLLLLLVFPATLLLRVGPGGSLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLAEDKEE
          M.SL.RLLLLLL.V.P.TLLLR.GPGGSLAVAQDLTEDEETVEDSII.DEDDEAEVEEDEPTDLAEDKEE
Retrocopy MRSLHRLLLLLL-VLPTTLLLRGGPGGSLAVAQDLTEDEETVEDSIIDDEDDEAEVEEDEPTDLAEDKEE

Parental  DDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTAL
          DDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQ.Y.FYIQNFTAL
Retrocopy DDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQNY*FYIQNFTAL

Parental  PLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFM
          PLNTVVPPQR.ATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFM
Retrocopy PLNTVVPPQR*ATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFM

Parental  YMFLAGLGLLVVVGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQET
          YMF.AGLG.LVVVGLHQLLESRKRKRPIQK.EMGTSSQNDVDMS.IPQET
Retrocopy YMFPAGLGQLVVVGLHQLLESRKRKRPIQKIEMGTSSQNDVDMS*IPQET

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	0.07 RPM	155.15 RPM
ERP005899_muscle	0.16 RPM	230.95 RPM
SRP017611_brain	0.27 RPM	164.40 RPM
SRP017611_kidney	0.30 RPM	270.81 RPM
SRP017611_liver	0.45 RPM	292.14 RPM
SRP030211_testis	0.20 RPM	206.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1285 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1285 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285 ,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850,