RetrogeneDB ID: retro_btau_1714

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:88159335..88160721(-)
• Located in intron of: ENSBTAG00000032007

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUSAP1
• Ensembl ID: ENSBTAG00000010774
• Aliases: None
• Description: Nucleolar and spindle-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q2YDJ0]

Sequence

>retro_btau_1714
ATGATCGTTCCCTCCCTGGAGGAGCTGAACTCCTTCAAGTACAGTGACCTGCAGAACTTGGCCAAGAGTCTGGGCCTCCG
GGCTAACCTCAGGGCAGACAAGCTGTTAAGGGCCTTAAAAGCTCATCTTAAAAATGAAGCAAGAAAAGAAAATGAAAATC
AGGATGAAATTCAAACTTCTGCATCCTCTTGTGATGAGCCTGAGATACAGACCAGCAGCCAGGAACAAGCTGAGAGGGAG
CCGGATGACCATGTCACCAAAACCAGAGGAAGGCGTAAGACTGTCCACAGGAGCCCTGACTCGCAGGCAAATGGAAATGT
GCAAACTGAAAAGAAGCTACCACCTGTGCCCAATCTGCAGAATCATTCAAAGATAAAACTATGTGGCCCTACTAAATCCC
AGAATCAAGAAAAGCATGAAAACCAGGTTCTCAGAACTGCTGTAGAAGTTCCTTCTCTACCCAATGAGAGTCAAGGAGAT
GAGAATACGGTGTCCTCAGGAAAACATGGAATAGATGGTAATGAAGATCCAAGGGTACCTTCAAAAAGAAAGAAGTCTCT
CTACACAGATGGGTTTTCCAAACCTGGAAAAAATAAAACTGCAAGCACTACTCCAAACTTTAAGAAGCTTCACGAGGCTC
GTTTTAAGGAAATGGAGTCCATTGATCAATATGTTGAGAGAAAAAAGAAACATTTTGAAGAACACAATTCATTTAATGAA
CTGAAGAGGCAGCCCGTCACTAAGGGAGTGCTGGCAACTCCAGTTCCTGCCCGAGGAAGACTCTCCGTGGCTTGTACCCC
TGGCAGCCAGCGGCGCTCGCAAGGCCAGCCCCACGCAGGCCGGAGCACCTTGTGTGTGAAGGGGTCAGCCAAGCGCTCTG
CTCTCTTGGCAGCTAAGATGAATGTCAGGTTTTCAGCTGCTACTAAAGATAATGAGCATAAGCGTTCACTGACCAAGACT
CCAGCCAGAAAGTCTCCACATGTGACCACGTCTGGGAATACCCCAAAAGGCCAGGCTGTGCTCGGGACACACAAGTTAAA
GACCACAAGGGGTGAATCTGTTGCTGTTATTACCCCATTCAAGTTGACAACTGAAGCAGCGCAGACTCCAATCTCCCATA
AAAAACCAGTGTTTGATCTCAAAGCAAATTTGTCTCGTCCTCTCAACTATGAGCCACACAAAGGAAAACTGAAACCATGG
GGACAGTCTAAAGAGAACAATTCTCTACATGAGCATGTCAACAGAGTTAGCTTCCACAAGAAAACTTATAAACAACCTCG
TCTCCAGACCAGGGAGGAGCAACGAAAGAAACATGAGCGGGAGCGAAAGGAGAAGAAAGAAAAGGTCCTGGGAGTTCGAA
GGGGCCTCATTATAGCTGAACGTTCA

Alignment

ORF - retro_btau_1714 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIVPSLEELNSFKYSDLQNLAKSLGLRANLRADKLLRALKAHLKNEARKENENQDEIQTSASSCDEPEIQ
          MIVPSLEELNSFKYSDLQNLAKSLGLRANLRADKLLRALKAHLKNEARKENENQDEIQTSASSCDEPEIQ
Retrocopy MIVPSLEELNSFKYSDLQNLAKSLGLRANLRADKLLRALKAHLKNEARKENENQDEIQTSASSCDEPEIQ

Parental  TSSQEQAEREPDDHVTKTRGRRKTVHRSPDSQANGNVQTEKKLPPVPNLQNHSEIKLCGPTKSQNQEKHE
          TSSQEQAEREPDDHVTKTRGRRKTVHRSPDSQANGNVQTEKKLPPVPNLQNHS.IKLCGPTKSQNQEKHE
Retrocopy TSSQEQAEREPDDHVTKTRGRRKTVHRSPDSQANGNVQTEKKLPPVPNLQNHSKIKLCGPTKSQNQEKHE

Parental  NQVLRTAVEVPSLPNESQGDENTVSSGKHGIDGNEDPRVPSKRKKSLYTDGFSKPGKNKTASTTPNFKKL
          NQVLRTAVEVPSLPNESQGDENTVSSGKHGIDGNEDPRVPSKRKKSLYTDGFSKPGKNKTASTTPNFKKL
Retrocopy NQVLRTAVEVPSLPNESQGDENTVSSGKHGIDGNEDPRVPSKRKKSLYTDGFSKPGKNKTASTTPNFKKL

Parental  HEARFKEMESIDQYVERKKKHFEEHNSFNELKVLQRQPVTKGVPATPVPARGRLSVACTPGSQRRSQGRP
          HEARFKEMESIDQYVERKKKHFEEHNSFNELK...RQPVTKGV.ATPVPARGRLSVACTPGSQRRSQG.P
Retrocopy HEARFKEMESIDQYVERKKKHFEEHNSFNELK---RQPVTKGVLATPVPARGRLSVACTPGSQRRSQGQP

Parental  HAGRSTLCVKGSAKRSALSAAKMNVRFSAATKDNEHKRSLTKTPARKSPHVTTSVNTPKGQAVLGTHKLK
          HAGRSTLCVKGSAKRSAL.AAKMNVRFSAATKDNEHKRSLTKTPARKSPHVTTS.NTPKGQAVLGTHKLK
Retrocopy HAGRSTLCVKGSAKRSALLAAKMNVRFSAATKDNEHKRSLTKTPARKSPHVTTSGNTPKGQAVLGTHKLK

Parental  TTRGESVAVITPFKLTTEASQTPISHKKPVFDLKASLSRPLNYEPHKGKLKPWGQSKENNSLHEHVNRVS
          TTRGESVAVITPFKLTTEA.QTPISHKKPVFDLKA.LSRPLNYEPHKGKLKPWGQSKENNSLHEHVNRVS
Retrocopy TTRGESVAVITPFKLTTEAAQTPISHKKPVFDLKANLSRPLNYEPHKGKLKPWGQSKENNSLHEHVNRVS

Parental  FHKKTYKQPRLQTREEQRKKHERERKEKKEKVLGVRRGLIIAERS
          FHKKTYKQPRLQTREEQRKKHERERKEKKEKVLGVRRGLIIAERS
Retrocopy FHKKTYKQPRLQTREEQRKKHERERKEKKEKVLGVRRGLIIAERS

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	3.10 RPM
ERP005899_muscle	0.32 RPM	13.99 RPM
SRP017611_brain	0.00 RPM	1.74 RPM
SRP017611_kidney	0.00 RPM	2.25 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP030211_testis	0.77 RPM	55.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1714 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1714 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714 ,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578,
Cavia porcellus	ENSCPOG00000012875	1 retrocopy	retro_cpor_993,
Cavia porcellus	ENSCPOG00000020956	1 retrocopy	retro_cpor_258,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088,