RetrogeneDB ID: retro_btau_1625

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:88081847..88083084(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006182
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA2
• Ensembl ID: ENSBTAG00000003757
• Aliases: None
• Description: DnaJ homolog subfamily A member 2 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJ94]

Sequence

>retro_btau_1625
ATGGCGAACGTGGCCGACACGAAACTGTACGACATCCTGGGCGTCCCGCCTGGAGCCAACGAGAACGAGCTGAAGAAGGC
ATACAGAAAGTTAGCCAAAGAATACCATCCTGATAAGAATCCAAATGCTGGTGACAAATTCAAAGAAATAAGCTTTGCAT
ATGAAGTACTATCAAATCCTGAGAAGCGCGAACTATATGACAGATATGGAGAACAAGGTCTTCGGGAGGGTAGCGGTGGA
GGTGGTGGCATGGATGATATTTTCTCTCACATCTTTGGTGGAGGATTATTTAACTTTATGGGTAATCAGAGCAGAAGTCG
AAATGGCAGAAGAAGAGGAGAAGACATGATGCATCCACTCAAAGTATCTTTAGAAGACCTGTATAATGGCAAGACAACCA
AACTACAGCTTAGCAAGAATGTACTCTGTAGTGCATGCAGTGGCCAAGGTGGGAAGTCTGGAGCTGTTCAGAAGTGTAGT
GCTTGTCGGGGTCGAGGTGTCCGCATCATGATCAGACAGCTGGCTCCAGGGATGGTGCAGCAGATGCAGTCTGTGTGTTC
TGACTGTAATGGAGAAGGAGAGGTAATTAATGAAAAGGACCGCTGTAAAAAATGTGAAGGGAAGAAAGTGATTAAAGAAG
TCAAGATTCTTGAAGTCCAGGTAGACAAAGGCATGAAACATGGGCAGAGAATTACGTTTACTGGGGAAGCAGACCAGGCC
CCAGGAGTGGAACCAGGAGACATTGTTCTTTTGCTACAAGAAAAAGAGCATGAGGTGTTCCAGAGAGATGGGAATGATTT
GCACATGACATATAAGATAGGACTTGTTGAAGCTCTTTGTGGGTTTCAGTTCACATTTAAGCACCTTGATGGACGTCAGA
TTGTGGTGAAATACCCCCCCTGGCAAAGTAATTGAACCAGGATGTGTTCGTGTAGTTCGAGGTGAAGGAATGCCACAATA
TCGTAATCCCTTTGAAAAAGGTGATCTTTACATAAAGTTTGATGTGCAGTTTCCTGAAAACAACTGGATCAACCCAGATA
AACTTTCTGAATTAAAAGATCTTCTGCCATCTAGACCAGAAGTTCCAAATATTATTGGAGACACTGAGGAGGTAGAGCTT
CAAGAATTTGATAGCACACGGGGCTCAGGAGGCGGCCAGAGGCGTGAAGCCTATAATGATAGCTCTGATGAAGAAAGCAG
TAGCCATCATGGACCAGGAGTGCAATGCGCCCATCAG

Alignment

ORF - retro_btau_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANVADTKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG
          MANVADTKLYDILGVPPGA.ENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG
Retrocopy MANVADTKLYDILGVPPGANENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG

Parental  EQGLREGSGGGGGMDDIFSHIFGGGLFSFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSKN
          EQGLREGSGGGGGMDDIFSHIFGGGLF.FMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSKN
Retrocopy EQGLREGSGGGGGMDDIFSHIFGGGLFNFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSKN

Parental  VLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGKKV
          VLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGKKV
Retrocopy VLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGKKV

Parental  IKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC
          IKEVKILEV.VDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC
Retrocopy IKEVKILEVQVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC

Parental  GFQFTFKHLDGRQIVVKY-PPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLS
          GFQFTFKHLDGRQIVVKY.PPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLS
Retrocopy GFQFTFKHLDGRQIVVKY>PPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLS

Parental  ELEDLLPSRPEVPNIIGDTEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ
          EL.DLLPSRPEVPNIIGDTEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ
Retrocopy ELKDLLPSRPEVPNIIGDTEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ

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	38.14 RPM
ERP005899_muscle	0.26 RPM	71.27 RPM
SRP017611_brain	0.78 RPM	53.17 RPM
SRP017611_kidney	0.24 RPM	45.11 RPM
SRP017611_liver	0.08 RPM	38.43 RPM
SRP030211_testis	2.54 RPM	124.65 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1625 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625 , retro_btau_798,
Bos taurus	ENSBTAG00000016265	6 retrocopies	retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778,