RetrogeneDB ID: retro_btau_1069

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:3373124..3373631(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000026400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.62733
• Ensembl ID: ENSBTAG00000016312
• Aliases: None
• Description: galectin-4 [Source:RefSeq peptide;Acc:NP_001029940]

Sequence

>retro_btau_1069
ATGGCCTTTGTCCCTGCACCAGGCTACCAGCCCACCTACAACCCGACACTGCCCTACCACAACCCCATCCCAGGAGGTCT
CAGAGTTGGAATGTCCATTTACATGCAAGGAGTGGCTAGCGAGCACATGAAGAGGTTCTTCGTGAACTTCGAGGTGGGGC
AGGGCCAAGGGGCAGACGTCGCTTTCCACTTCAATCCCCGCTTTGATGGCTGGGATAAGGTGGTCTTGAACTCGAAGCAG
AATGGCTCGTGGGGCAACGAGGAGAGGAAAATGAGCATGCCCTTCCGCAAGGGTGCGGCCTTCGAGCTGGTGTTCATGGT
CATGATGGAGCACTTCAAGGTGGTGGTGAATGGGACTCCCTTCCATGAGTTTAAGCACCGGATCCCGCTGCAGATGGTCA
CCCACCTGCATGTGGATGGCGACCTGATGCTTCAATCAATTAACTTCATTGGAGGCCAGCCCCCCTCAAACCAGATGCCC
ATGCCTGCTAAGGCGTACCCAAGTCCC

Alignment

ORF - retro_btau_1069 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMSVYIQGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG
          MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMS.Y.QGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG
Retrocopy MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMSIYMQGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG

Parental  WDKVVLNSKQNGSWGQEERKMSMPFRKGAAFELVFMVMTEHFKVVVNGTPFYEFKHRILLQMVTHLHVDG
          WDKVVLNSKQNGSWG.EERKMSMPFRKGAAFELVFMVM.EHFKVVVNGTPF.EFKHRI.LQMVTHLHVDG
Retrocopy WDKVVLNSKQNGSWGNEERKMSMPFRKGAAFELVFMVMMEHFKVVVNGTPFHEFKHRIPLQMVTHLHVDG

Parental  DLMLQSINFIGGQPPSNQMPMPAQAYPMP
          DLMLQSINFIGGQPPSNQMPMPA.AYP.P
Retrocopy DLMLQSINFIGGQPPSNQMPMPAKAYPSP

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	0.79 RPM	23.36 RPM
ERP005899_muscle	20.27 RPM	892.08 RPM
SRP017611_brain	0.14 RPM	28.28 RPM
SRP017611_kidney	0.06 RPM	11.62 RPM
SRP017611_liver	0.68 RPM	39.87 RPM
SRP030211_testis	0.16 RPM	3.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1069 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Bos taurus	ENSBTAG00000016312	1 retrocopy	retro_btau_1069 ,