RetrogeneDB ID: retro_btau_1451

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:35008570..35010337(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000045523
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FARSB
• Ensembl ID: ENSBTAG00000011649
• Aliases: None
• Description: phenylalanyl-tRNA synthetase beta chain [Source:RefSeq peptide;Acc:NP_001098491]

Sequence

>retro_btau_1451
ATGCCGACTGTCAGCGTGAAGTGAGATCTGCTCTTCCGAGCCCTGGGCCGGACCTACACTGATGAAGAATTTGATGAACT
GTGCTTTGAATTTGGACTGGAACTTGATGAAATTACATCTGAAAAGGAAATTATAAGTAAGGAACAAGGTAATGAAAAGG
CCCATGGGGCCTCTGATGTTGTTCTCTACAAAATTGACGTCCCTGCCAATAGATATGACCTGCTGTGTCTGGAAGGATTG
GTTCGAGGACTTCAAGTCTTCAAAGAAAGGATAAAGACTCCGATGTATAAACGGGTAATGCCTAAAGGAGAAATCCAGAA
GTTGATCATCACAGAAGAGACAGCTAAAATACGCCCGTACACTGTTGCAGCGGTTCTCCGAAACATAAAGTTTACAAAAG
ATAGATATGACAGCTTCATTGAACTTCAGGAGAAATTACATCAGAACATTTGCAGGAAAAGAGCCTTGGTTGCTATTGGT
ACCCATGATTTGGACACTTTGTCAGGTCCATTTACTTACACTGCAAAGAAACCTTCTGATATCAAATTCAAGCCTCTAAA
TAAGAGTAAAGAGTATACAGCCTGTGAACTGATGAACATATACAAGACTGACAACCAGCTTAAACATTATTTACATATAA
TTGAAAATAAACCTCTGTACCCAGTTATCTATGATAGCAAAGGTGTCGTCCTTTCCATGCCTCCAATCATCAACGGAAAC
CATTCCAAAATAACAGTAAATACGAAAAATGTATTTATTGAGTGCACAGGAACTGACTTTACTAAGGCAAAAATAGTTCT
TGATGTCATTGTTACCACGTTCAGTGAATATTGTGAGAATCAGTTTACGGTTGAAGCAGCTGAGGTAGTTTTTCCTAATG
GAAAATTACATACCTTTCCAGAACTGGCTTATCGAAAGGAGATGGTGAGAGCTGACCTAATTAACAAAAAAGTTGGGATC
AGAGAAACTCCAGAAAATCTTGCCAAGCTTCTGACCAGGATGTGTTTAAAGTCAGAAGTCATAGGCGATGGGAATCAGAT
CGAGGTTGAAATCCCCCCGACCAGAGCTGACATTATCCACGCCTGTGATATCATAGAAGACGCAGCTATTGCTTACGGAT
ATAACAACATTCAGATGACTCTCCCGAAAACGTACACCATAGCTAATCAATTTCCCCTAAATAAACTCACAGAACTCCTG
AGACAGGACATGGCAGCTGCCGGATTCACCGAAGCACTTACCTTTGCTCTGTGCTCCCAAGAAGATATTGCTGACAAACT
GGGTATGGATATCTCTGCAACCAAGGCCGTCCACATAAGTAATCCTAAAACGGCTGAATTCCAGGTGGCACGCACTACCC
TTCTTCCTGGCCTCCTCAAGACCCTAGCTGCCAATCGGAAGACGCCACTTCCTCTGAAGCTGTTTGAAATTTCTGACATT
GTAATAAAAGATTCTAGCAGAGATGTGGGTGCAAGAAACTACAGGCATCTCTGTGCTGTTTATTACAACAAGAATCCTGG
GTTTGAGATAATCCATGGGCTTCTGGATAGAATCATGGAGCTGCTTGACGTGCCTCCTGGTGAAAAGAAGGGAGGATATG
CAATCAAAGCATCAGAAGGCCCTGTGTTCTTTCCTGGGCGATGTGCAGAGATCTTTGCCCGGGGCCAGAGCATCGGGAAG
CTGGGGGTCCTTCATCCCGACGTTATCACCAAGTTCGAGCTGACTATGCCCTGCTCCTGCGTGGAAATCAACATTGAGCC
ATTTTTG

Alignment

ORF - retro_btau_1451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPTVSVKRDLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN
          MPTVSVK.DLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN
Retrocopy MPTVSVK*DLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN

Parental  RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPYAVAAVLRNIKFTKDRYDSFI
          RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPY.VAAVLRNIKFTKDRYDSFI
Retrocopy RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPYTVAAVLRNIKFTKDRYDSFI

Parental  ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY
          ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY
Retrocopy ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY

Parental  LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN
          LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN
Retrocopy LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN

Parental  QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE
          QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE
Retrocopy QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE

Parental  IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ
          IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ
Retrocopy IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ

Parental  EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRKMPLPLKLFEISDIVIKDSSRDVG
          EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRK.PLPLKLFEISDIVIKDSSRDVG
Retrocopy EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRKTPLPLKLFEISDIVIKDSSRDVG

Parental  ARNYRHLCAVYYNKNPGFEIIHGLLDRIMQLLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK
          ARNYRHLCAVYYNKNPGFEIIHGLLDRIM.LLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK
Retrocopy ARNYRHLCAVYYNKNPGFEIIHGLLDRIMELLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK

Parental  LGVLHPDVITKFELTMPCSCVEINIEPFL
          LGVLHPDVITKFELTMPCSCVEINIEPFL
Retrocopy LGVLHPDVITKFELTMPCSCVEINIEPFL

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	1.23 RPM	10.24 RPM
ERP005899_muscle	0.32 RPM	43.81 RPM
SRP017611_brain	1.42 RPM	19.05 RPM
SRP017611_kidney	0.65 RPM	23.06 RPM
SRP017611_liver	0.76 RPM	12.76 RPM
SRP030211_testis	0.43 RPM	31.73 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

13 EST(s) were mapped to retro_btau_1451 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB532909	35008720	35009110	97.7	381	9	372
CK960751	35008997	35009693	100	696	0	696
DY058326	35009393	35009664	100	271	0	271
DY070806	35009374	35009597	100	223	0	223
DY117886	35009312	35009663	100	351	0	351
EE909578	35009105	35009629	100	524	0	524
EE909826	35009105	35009712	100	607	0	607
EE909830	35009105	35009564	100	459	0	459
EE909852	35009105	35009684	100	578	0	578
EW740015	35009050	35009230	98.4	177	3	174
GO352920	35009050	35009228	99.5	177	1	176
GO353727	35009050	35009228	99.5	177	1	176
GO353770	35009228	35009723	99.8	494	1	493

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1451 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011649	1 retrocopy	retro_btau_1451 ,
Felis catus	ENSFCAG00000026772	1 retrocopy	retro_fcat_1179,
Gorilla gorilla	ENSGGOG00000017051	1 retrocopy	retro_ggor_598,
Pteropus vampyrus	ENSPVAG00000006985	1 retrocopy	retro_pvam_804,