RetrogeneDB ID: retro_btau_847

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:136768698..136770669(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRP1
• Ensembl ID: ENSBTAG00000021838
• Aliases: ESRP1, RBM35A
• Description: epithelial splicing regulatory protein 1 [Source:RefSeq peptide;Acc:NP_001179931]

Sequence

>retro_btau_847
ATGACGGCGTCTCCGGATTACTTGGTGGTGCTCTTCGGAATCACGGCTGGGGCCACCGGGGCCAAGCTGGGCTCGGACGA
GAAGGAGCTGATCCTGCTCTTATGGAAAGTCGTGGATCTGGCCAACAAGAAGGTGGGACAGTTGCACGAAGTACTAGTTA
GACCGGATCACTTGGACCTGACGGAGGACTGCAAAGAAGAAACGAAGCTCGACGCCGAGAGCCTGTCCTCGGCGCCGCAG
CTGGACCAAGCGCTCCGACAGTTTAACCAGTCAGTGAGCAATGAACTGAATATTGGGGTAGGAACCTCCTTCTGTCTCTG
TACCGACGGGCAGCTTCATGTCAGGCAAATTCTGCATCCTGAGGCTTCTAAGAAGAATGTATTATTGCCTGAATGCTTCT
ATTCCTTTTTTGATCTTCGAAAAGAATTCAAGAAGTGTTGCCCTGGTTCACCTGATATTGATAAACTGGATGTTGCAGCA
ATGATAGAGGGTTTAAATTTTGAGAAGAATAGTTCAGTCTCCCGGTATGGAGCATCTCAAGTTGAAGATATGGGAAATAT
AATCTTAGCAATGATTTCAGACCCTTATAATCACAGGTTTTCAGATCCAGAGAGAGTAAATTACAAATTTGAAAGTGGCA
CTTGCAGCAAGATGGAACTTATTGATGACAACACAGTAGTCAGGGCACGAGGTTTACCATGGCAGTCTTTGGATCAAGAT
ATTGCAAGATTCTTCAAAGGACTCAATATTGCCAAGGGCGGTGCAGCACTTTGTCTGAATGCCCAGGGTCAGAGGAACGG
AGAAGCCCTGGTTAGGTTTGTGAGTGAGGAGCACAGAGACCTAGCTCTGCAGAGACACAAGCACCACATGGGGAGCCGGT
ACATTGAGGTTTACAAAGCAACAGGTGAAGATTTTCTTAAAATTGCTGGTGGTACATCCAATGAGGTGGCCCAGTTTCTC
TCCAAGGAAAACCAAGTCATTGTCCGCATGCGGGGGCTCCCCTTCACGGCCACGGCTGATGAAGTGGTGGCCTTCTTTGG
ACAGCATTGCCCCATCACTGGGGGGAAGGAAGGCATCCTCTTTGTTACCTACCCGGATGGTAGGCCCACAGGGGATGCTT
TTGTCCTCTTTGCTTGCGAGGAATACGCACAGAACGCACTGAGGAAGCATAAAGACTTGTTGGGTAAAAGATACATCGAA
CTCTTCAGGAGCACAGCAGCTGAAGTTCAGCAGGTGCTGAATCGATTCTCCTCGGCTCCTCTCATTCCACTTCCAACCCC
TCCCATTATTCCAGTACTACCTCAGCAGTTTGTGCCCCCTACAAACATTAGAGACTGTATACGCCTTCGAGGTCTTCCCT
ATGTAGCCACAACTGAGGATATCCTTGACTTCCTGGGGGAGTTTTCCACCGATATCCGAACTCATGGGGTCCACATGGTA
TTGAACCATCAGGGCCGCCCATCGGGAGATGCCTTTATCCAGATGAAGTCTGCGGACAGAGCATTTATGGCTGCACAGAA
GTGTCATAAAAAAACCATGAAGGACAGATATGTTGAAGTCTTTCAGTGTTCAGCTGAGGAGATGAACTTTGTGTTAATGG
GGGGCACTTTAAATCGAAATGGCTTATCCCCACCGCCATGTAAGTTACCATGCCTGTCCCCTCCCTCCTACACATTTCCA
GCTCCCGCAGCAGTTATTCCTACTGAAGCTGCCATTTACCAGCCCTCAGTGCTCCTGAACCCACGAGCGCTGCAGCCCTC
CACAGCGTACTACCCCGCGGGCACCCAGCTCTTCATGAACTACACGGCGTACTACCCCAGCCCCCCAGGTTCGCCCAATA
GTCTTGGCTACTTCCCTACAGCTGCTAATCTTAGCGGTGTCCCTCCACAGCCTGGCACGGTGGTCAGAATGCAGGGCCTG
GCCTACAATACTGGAGTTAAGGAAATTCTTAACTTCTTCCAAGGTTACCAG

Alignment

ORF - retro_btau_847 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.17 %
• Parental protein coverage: 96.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTASPDYLVVLFGITAGATGAKLGSDEKELILLLWKVVDLANKKVGQLHEVLVRPDHLELTEDCKEETKL
          MTASPDYLVVLFGITAGATGAKLGSDEKELILLLWKVVDLANKKVGQLHEVLVRPDHL.LTEDCKEETKL
Retrocopy MTASPDYLVVLFGITAGATGAKLGSDEKELILLLWKVVDLANKKVGQLHEVLVRPDHLDLTEDCKEETKL

Parental  DAESLSSAPQLDQALRQFNQSVSNELNIGVGTSFCLCTDGQLHVRQILHPEASKKNVLLPECFYSFFDLR
          DAESLSSAPQLDQALRQFNQSVSNELNIGVGTSFCLCTDGQLHVRQILHPEASKKNVLLPECFYSFFDLR
Retrocopy DAESLSSAPQLDQALRQFNQSVSNELNIGVGTSFCLCTDGQLHVRQILHPEASKKNVLLPECFYSFFDLR

Parental  KEFKKCCPGSPDIDKLDVAAMTECLNFEKNSSASRYGASQVEDMGNIILAMISDPYNHRFSDPERVNYKF
          KEFKKCCPGSPDIDKLDVAAM.E.LNFEKNSS.SRYGASQVEDMGNIILAMISDPYNHRFSDPERVNYKF
Retrocopy KEFKKCCPGSPDIDKLDVAAMIEGLNFEKNSSVSRYGASQVEDMGNIILAMISDPYNHRFSDPERVNYKF

Parental  ESGTCSKMELIDDNTVVRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVSEEHRD
          ESGTCSKMELIDDNTVVRARGLPWQS.DQDIARFFKGLNIAKGGAALCLNAQG.RNGEALVRFVSEEHRD
Retrocopy ESGTCSKMELIDDNTVVRARGLPWQSLDQDIARFFKGLNIAKGGAALCLNAQGQRNGEALVRFVSEEHRD

Parental  LALQRHKHHMGSRYIEVYKATGEDFLKIAGGTSNEVAQFLSKENQVIVRMRGLPFTATADEVVAFFGQHC
          LALQRHKHHMGSRYIEVYKATGEDFLKIAGGTSNEVAQFLSKENQVIVRMRGLPFTATADEVVAFFGQHC
Retrocopy LALQRHKHHMGSRYIEVYKATGEDFLKIAGGTSNEVAQFLSKENQVIVRMRGLPFTATADEVVAFFGQHC

Parental  PITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSAP
          PITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSAP
Retrocopy PITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSAP

Parental  LIPLPTPPIIPVLPQQFVPPTNIRDCIRLRGLPYAATIEDILDFLGEFSTDIRTHGVHMVLNHQGRPSGD
          LIPLPTPPIIPVLPQQFVPPTNIRDCIRLRGLPY.AT.EDILDFLGEFSTDIRTHGVHMVLNHQGRPSGD
Retrocopy LIPLPTPPIIPVLPQQFVPPTNIRDCIRLRGLPYVATTEDILDFLGEFSTDIRTHGVHMVLNHQGRPSGD

Parental  AFIQMKSADRAFMAAQKCHKKTMKDRYVEVFQCSAEEMNFVLMGGTLNRNGLSPPPC----LSPPSYTFP
          AFIQMKSADRAFMAAQKCHKKTMKDRYVEVFQCSAEEMNFVLMGGTLNRNGLSPPPC....LSPPSYTFP
Retrocopy AFIQMKSADRAFMAAQKCHKKTMKDRYVEVFQCSAEEMNFVLMGGTLNRNGLSPPPCKLPCLSPPSYTFP

Parental  APAAVIPTEAAIYQPSVLLNPRALQPSTAYYPAGTQLFMNYTAYYPSPPGSPNSLGYFPTAANLSGVPPQ
          APAAVIPTEAAIYQPSVLLNPRALQPSTAYYPAGTQLFMNYTAYYPSPPGSPNSLGYFPTAANLSGVPPQ
Retrocopy APAAVIPTEAAIYQPSVLLNPRALQPSTAYYPAGTQLFMNYTAYYPSPPGSPNSLGYFPTAANLSGVPPQ

Parental  PGTVVRMQGLAYNTGVKEILNFFQGYQ
          PGTVVRMQGLAYNTGVKEILNFFQGYQ
Retrocopy PGTVVRMQGLAYNTGVKEILNFFQGYQ

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	0.87 RPM
ERP005899_muscle	3.48 RPM	62.34 RPM
SRP017611_brain	0.32 RPM	0.09 RPM
SRP017611_kidney	0.89 RPM	15.23 RPM
SRP017611_liver	0.00 RPM	0.30 RPM
SRP030211_testis	0.04 RPM	2.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_847 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EV659943	136769838	136770019	96.1	171	7	161

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_847 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Bos taurus	ENSBTAG00000020513	1 retrocopy	retro_btau_42,
Bos taurus	ENSBTAG00000021838	1 retrocopy	retro_btau_847 ,
Canis familiaris	ENSCAFG00000009305	1 retrocopy	retro_cfam_1096,