RetrogeneDB ID: retro_btau_1555

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:9822765..9823347(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.48519
• Ensembl ID: ENSBTAG00000033727
• Aliases: None
• Description: RNA-binding protein with multiple splicing [Source:RefSeq peptide;Acc:NP_001040000]

Sequence

>retro_btau_1555
CTCTCTGTCAGCGGTCTCCCTCTGGACATCAAACCTCGGGAGCTATATCTGCTTTTCAGACCATTTAAGGGCTACGAAGG
TTCTCTTATAAAGCTCACATCTAAGCAGCCCGTAGGTTTTGTCAGTTTTGACAGTCGCTTAGAAGCAGAAGCTGCCAAGA
ATGCTTTGAATGGCATCCGCTTCGATCCTGAAATTCCGCAAACACTATGACTAGAGTTTGCTAAGGCAAACACGAAGATG
GCCAAGAACAAACTAGTAGGGACTCCAAACCCTAGTACTCCTCTGCTCAACACTGTACCTCAGTTCATTGCCAGAGAGCC
ATATGAGCTCACAGTGCCTGCACTTTACCCCAGTAGCCCTGAAGTGTGGGCCCCGTACCCTCTGTACCCAGCGGACTTAG
CGCCTGTGCTGCCTCCTCCTGCTTTCACCTACCCCGCTTCACTGCATGCCCAGTGTTTCTCTCCTGAGGCAAAGCCCAAC
ACACCTGTCTTTTGTCCACTTCTCCAGCAAATTAGATTTGTCTCTGGGAATGTGTTTGTAACATATCAACCTACTGCAGA
CCAGCAAAGGGAGCTCCCATGT

Alignment

ORF - retro_btau_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 88.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLR
          L.VSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSR.EAEAAKNALNGIRFDPEIPQTL.
Retrocopy LSVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRLEAEAAKNALNGIRFDPEIPQTL*

Parental  LEFAKANTKMAKNKLVGTPNPSTPLPNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPADLAPALPPP
          LEFAKANTKMAKNKLVGTPNPSTPL.NTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPADLAP.LPPP
Retrocopy LEFAKANTKMAKNKLVGTPNPSTPLLNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPADLAPVLPPP

Parental  AFTYPASLHAQCFSPEAKPNTPVFCPLLQQIRFVSGNVFVTYQPTADQQRELPC
          AFTYPASLHAQCFSPEAKPNTPVFCPLLQQIRFVSGNVFVTYQPTADQQRELPC
Retrocopy AFTYPASLHAQCFSPEAKPNTPVFCPLLQQIRFVSGNVFVTYQPTADQQRELPC

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	0.36 RPM	8.22 RPM
ERP005899_muscle	0.00 RPM	8.66 RPM
SRP017611_brain	0.05 RPM	1.19 RPM
SRP017611_kidney	0.53 RPM	39.53 RPM
SRP017611_liver	0.08 RPM	6.19 RPM
SRP030211_testis	0.04 RPM	12.56 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1555 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1555 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
Ailuropoda melanoleuca	ENSAMEG00000001522	1 retrocopy	retro_amel_905,
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Bos taurus	ENSBTAG00000033727	1 retrocopy	retro_btau_1555 ,
Callithrix jacchus	ENSCJAG00000012366	1 retrocopy	retro_cjac_2705,
Tarsius syrichta	ENSTSYG00000013982	2 retrocopies	retro_tsyr_1171, retro_tsyr_1397,