RetrogeneDB ID: retro_btau_1447

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:10923551..10924137(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009280
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSBTAG00000015901
• Aliases: None
• Description: Armadillo repeat-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBE1]

Sequence

>retro_btau_1447
GCTTTTCGATACTTGGCAGAGTACCATGCCAACAGAGAAAAGATGAAAGGAGAGTTGGGAAAGATGTTAAGCTTGCAAAA
TGTTATACAGAAATCTACAATTCCAGGGGAAACAAAACTGCTAGCCTCTGAAATCGATGACATTCTTCAATCTTCCAATA
TGGCAGTTGGGGATAGTTTCAATGAAATGAATTCATGTCGAAGGAAAGCTCAGTTTTTTGGGGGGGACTACAAACAAATG
TGCCAAAACAGTGGTTTTGCATATAGATAGTCTTGATGATATGTCCCTGTGTGAAGTGGCCTTGTTAAAAATTAAAGGCG
TTATTAGCTTTACTTTTCAAATGGCCGTTCAGAGATGTGTGGTGCGAATCCATTCAGATCGTAAAGCTTTGGCATCAGCA
ATAGCATCAACCCAGTTTATGAAGGCTCAGCAAGTTGTGAAGAGCAAAAGTGGAGAAGAGATACTAGTCCCATTCCAGGA
CACACCTGTGGAGGTAGAACAGAACACGGAGCTGCCTGACTACCTGCCCGAGCATGAGAGTCCCACAAAGGAGCAAGACA
AAGTGGGCAGGACAAGGCGGTATCCC

Alignment

ORF - retro_btau_1447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.16 %
• Parental protein coverage: 71.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALRYLAECRANREKMKGELGMMLSLQNVIQKSTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKA
          A.RYLAE..ANREKMKGELG.MLSLQNVIQKST.PGETKLLASEI.DILQSSNMA.GDSFNEMNS.RRKA
Retrocopy AFRYLAEYHANREKMKGELGKMLSLQNVIQKSTIPGETKLLASEIDDILQSSNMAVGDSFNEMNSCRRKA

Parental  QFF-LGTTNKRAKTVVLHIDGLDDTSRRNLCEEALLKIKGVISFTFQMAVQRCVVRIRSDLKAEALASAI
          QFF..GTTNK.AKTVVLHID.LDD.S...LCE.ALLKIKGVISFTFQMAVQRCVVRI.SD.K..ALASAI
Retrocopy QFF>GGTTNKCAKTVVLHIDSLDDMS---LCEVALLKIKGVISFTFQMAVQRCVVRIHSDRK--ALASAI

Parental  ASTKVMKAQQVVKSESGEEMLVPFQDTPVEVEQNTELPDYLPEDESPTKEQDKAVSRVGSHP
          AST..MKAQQVVKS.SGEE.LVPFQDTPVEVEQNTELPDYLPE.ESPTKEQDK.V.R....P
Retrocopy ASTQFMKAQQVVKSKSGEEILVPFQDTPVEVEQNTELPDYLPEHESPTKEQDK-VGRTRRYP

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	21.34 RPM
ERP005899_muscle	0.00 RPM	23.60 RPM
SRP017611_brain	0.00 RPM	54.59 RPM
SRP017611_kidney	0.00 RPM	33.67 RPM
SRP017611_liver	0.00 RPM	16.76 RPM
SRP030211_testis	0.07 RPM	23.53 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1447 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1447 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447 ,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,