RetrogeneDB ID: retro_btau_463

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:19400263..19401151(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047343
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TATDN1
• Ensembl ID: ENSBTAG00000033446
• Aliases: None
• Description: Putative deoxyribonuclease TATDN1 [Source:UniProtKB/Swiss-Prot;Acc:Q148G4]

Sequence

>retro_btau_463
ATGAGTCATTTCAAATTTGTGGATATTGGTATCAACTTGACAGATCCTACGTTCAGAGGAATTTATAGGGTGGTTCAAAA
GCATCAAGATGACTTAAAGGACGGAAAAGAGAGAGCTGTTCAGATTGGTGTTAAAAAGTTTATGATTACAGGTGGAAATC
TATAAGACAGTAAAGATGCACTGCATTTGGCATAAACAAATGATATGTTTTTCGGCACCGTTGGGTGTCATCCTACAAGA
TGTGATGAATTCGAAAAGAATGACCCTGATCATTACCTGATGGAGTTGCTGAATCTTGCTGAAAGCAACAGGGAAAGTTG
TAGCCATAGGGGAATGTGGACTTGATTTTGACCGACTACAGTTTTGTTCCAAAGATACTCAGCTCAAGTATTTTGAAAAA
CAGTTTGAACTGTCAGAACAAACGAAATTACCCATGTTTCTCCATTGTCGGAACTCACATGCTGAATTTTTGGATATAAT
GAGAAGAAACAGAGATCGGTGTGTAGGTGGAGTGGTGCATTCATTTGAAGGTACCAAGGAAGCAGCAGCTGCTTTGATGG
ACTTGGGTCTCTATATAGGGTTTAATGGTTGCTCACTGAAAACTGAGGCTGATTTGGAAGTTATAAATCAATACCTAGTG
AAAAATTAATGATTGAGACTGATGCACCTTGGTGTGGAGTCAAAAGTACACATGCTGGATCAAAATATATAAAAACTTCA
TTTCCTACCAAAAAGAAGTGGGAAAACGGGCACTGTTTGAAAGACAGAAATGAACCCTGCCACATAATTCAAATACTGGA
GATAAAGTCAGCAGTAAGAGATGAAGATCCACTGGAACTAGCCAATACACTATATAACAACACTATTAAAATAGTTTTTC
CTGATATG

Alignment

ORF - retro_btau_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRFKFVDIGINLTDPMFRGIYRGVQKHQDDLQDVIERAVQIGVKKFMITGGNLQDSKDALHLAQTNDMF
          MS.FKFVDIGINLTDP.FRGIYR.VQKHQDDL.D..ERAVQIGVKKFMITGGNL.DSKDALHLA.TNDMF
Retrocopy MSHFKFVDIGINLTDPTFRGIYRVVQKHQDDLKDGKERAVQIGVKKFMITGGNL*DSKDALHLA*TNDMF

Parental  FSTVGCHPTRCDEFEKNDPDHYLMELLNLAESNK-GK-VVAIGECGLDFDRLQFCSKDTQLKYFEKQFEL
          F.TVGCHPTRCDEFEKNDPDHYLMELLNLAESN..GK.VVAIGECGLDFDRLQFCSKDTQLKYFEKQFEL
Retrocopy FGTVGCHPTRCDEFEKNDPDHYLMELLNLAESNR<GK<VVAIGECGLDFDRLQFCSKDTQLKYFEKQFEL

Parental  SEQTKLPMFLHCRNSHAEFLDIMRRNRDRCVGGVVHSFDGTKEAAAALMDLGLYIGFNGCSLKTEANLEV
          SEQTKLPMFLHCRNSHAEFLDIMRRNRDRCVGGVVHSF.GTKEAAAALMDLGLYIGFNGCSLKTEA.LEV
Retrocopy SEQTKLPMFLHCRNSHAEFLDIMRRNRDRCVGGVVHSFEGTKEAAAALMDLGLYIGFNGCSLKTEADLEV

Parental  L-KSIPSEKLMIETDAPWCGVKNTHAGSKYIKTSFPTKKKWENGHCLKDRNEPCHIIQILEIMSAVRDED
          ..KSIPSEKLMIETDAPWCGVK.THAGSKYIKTSFPTKKKWENGHCLKDRNEPCHIIQILEI.SAVRDED
Retrocopy I<KSIPSEKLMIETDAPWCGVKSTHAGSKYIKTSFPTKKKWENGHCLKDRNEPCHIIQILEIKSAVRDED

Parental  PLELANTLYNNTIKIFFPDM
          PLELANTLYNNTIKI.FPDM
Retrocopy PLELANTLYNNTIKIVFPDM

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	0.00 RPM	27.76 RPM
ERP005899_muscle	0.11 RPM	24.81 RPM
SRP017611_brain	0.09 RPM	8.86 RPM
SRP017611_kidney	0.06 RPM	15.88 RPM
SRP017611_liver	0.00 RPM	7.17 RPM
SRP030211_testis	0.03 RPM	10.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_463 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_463 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033446	1 retrocopy	retro_btau_463 ,
Homo sapiens	ENSG00000147687	1 retrocopy	retro_hsap_578,
Gorilla gorilla	ENSGGOG00000015875	1 retrocopy	retro_ggor_514,
Nomascus leucogenys	ENSNLEG00000005467	1 retrocopy	retro_nleu_804,
Oryctolagus cuniculus	ENSOCUG00000017403	1 retrocopy	retro_ocun_730,
Rattus norvegicus	ENSRNOG00000047198	1 retrocopy	retro_rnor_1737,
Tupaia belangeri	ENSTBEG00000006179	1 retrocopy	retro_tbel_707,