RetrogeneDB ID: retro_btau_1000

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:53923865..53926065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000048004
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP88
• Ensembl ID: ENSBTAG00000011507
• Aliases: None
• Description: nuclear pore complex protein Nup88 [Source:RefSeq peptide;Acc:NP_001029394]

Sequence

>retro_btau_1000
GGCGCCGAAGGCGGCCCCGGGGACGGTGAGCTGCGGCCTACCTGGCTGCCCAACCACGCCGTGTTCTTGCGGCTCCGAGA
GGGACGGAAAAACCAGAGCTCAGCTGAACCCGAGAAGCCAGCTTCATCATTGCCTTCGTCGCCGCCACTGCCTCCTCAGC
TGTTGATGAGAAAGCTGGTCTTGGGCCTCGCAGAGAGCTCTTTCTGTGGGGCGCAGAAGACAGCGCCTTCTTAGTCATGC
GCCTTCGGGGCCCCAGCTGCGCCGGTGAGGAGCCCTCCCTCTCGCAGTACCGGAGACGGCTTTGCATAAATGCACCCCTG
TTTGAAATCTATCAAGCCTTGTTAAGCCCAGCACAACATCATGTAGCATCATGTAGGAATAAAAGGACTTATATTAGAAT
TACCTAAAAGATGGGGAAAGAATTCTGAATTTGAAGGTGGAAAATCAGCAGTGAATTGTAGCACGACTCCCGTTGCTGAG
AGATTTTTCACCAGTTCAACCTCTCTGACTCTGAAGCATGTTGCCTGGTATCCGAGAGAGTTGCTAGATACTCAAATTGT
GCCGTTAACGTCAGACAACGTCATAAGAATTTACCCTTTGCGTATGACTAAGGTCATCGTACTTTCAGAAGCAGAAGAGG
AAAGTCTCATACTCAACAAAGGAAGGGCCTACACAGCATCTCTGGAAGAGACAGCAGTTGCATTTGACTTTGGGCCATTG
TCAGCAGTCCCAAAGCACATATTTGGATGAAAAGGCAAAGAAGAAGTAGTGGCTACTCCCTGTACATCTTATATGAAAAT
GAGGAGACTTTCCTTACGTTTGTTAGTCTGTTGCACAGCCCTGGGAGTGTGGGTAAGCTATTCGGCCCGTTGCCCATGCA
TCCTGCTGTTGAAGATAACTATGGCTACCATGCTTGTGCTGTGCTTTGCTTACCATGTGTCGCCAACATCCTGGTGATTA
CTACTGAGTCAGGAATGCTTCATTATTGCGTTGTGCTGGAGGGGGAAGAAGAAGATGACCACACATCAGAAAAGTCCTGG
GATTCCAGGGCTGACCTCATTCCATCACTGTATGTGTTTGAGTGTGTTGAGTTGGAGCTTGCTCTGAAATTGGCATCCGG
AGAGGATGAGCCCTTTGATTCTGACTTTTCTTGTCCATTGAAACTTCATAGAGATCCCAAGTGTCCCTTAAGATTCCACT
ATACTCATTAAGCTGCTGTACATAGTGTTGGGCTACCTTGGATTCATAAACTTCACAAGTTTCTTGGATCAGATGAAGAA
GACAAGGACAGTTTACAGGAACTGGCTACAGAACAGAAGTGCTTTGTACAGCACATTCTTTGTAGGAAGCCACTGCCATG
CAGTCAGCCAGCTCCTTTTCAAGGATCTGGATCATCCCTGACATCCTGGGGCCAACAGTGATCTGCATCACCAGTACCTA
TGAATACCTCCTCAGGCCTTTACTAAGCACAGTCCATCTAGCATCTCCTCCCCTGCTTTGTACCCGAGAAGATGTTGAAA
TGGCAGAGTCTCCCCTCCGTATTCTGGCTGAAACCCCGGATTCCTTTGAAAAGCATATTAGAAGCATTTGCAACGTGGTG
TTGCAAATCCAGCATTTTTGAAATCATCTGAAAAAGATACGGCTCCTCCTCCCAAAGAATGTCTTCAGCTCATCAGCAGA
GCCACCCACGTGTTCAGGAAATACTACATTCTTAAACAGGACCCGGCAAATGAGGAGATTCAGTGGAGGGTCAAATTGTT
GTGTGACTAAAAAAGAAACAATTAGAAGATCTCAATTACTGTTGCGAGGAGAGGAAAAGTCTACGGGAAATGGCTGAGCG
CTTAGCTGACAAATATGAGGAAGCCAAGGAAAAACAAGAAGACATCATGAACAGAATGAAAAAAGTACTTCACAGTTTTC
AGTCTCAGCTCCCAGTTCTCTCTGACAGTGAGAGAGACACGAAGAAAGAATTATAGCGATACCTCATCAACTTCAACATT
TGGGCAATGCTGTCAAATGGGTTACTATGAAAAAAGACTATCAACAACGAAAGATGGAAAAGGTACTGAGTCCTCAAAAG
CCCACCATTACTCTCAGCACCTACCAGTGGAAATGCATTCAGTCCATCCTGAAGGAGAAGGGTGAGCACATAAGAGAAAT
GGTGAAGCAAATTAATGGCATCTGAAATCATGTAAACTTC

Alignment

ORF - retro_btau_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GAEGGPGDGELWQTWLPNHAVFLRLREGLKNQSSTETEKPASSLPSSPPLPPQLLTRNLVLGLGG-ELFL
          GAEGGPGDGEL..TWLPNHAVFLRLREG.KNQSS.E.EKPASSLPSSPPLPPQLL.R.LVLGL...ELFL
Retrocopy GAEGGPGDGELRPTWLPNHAVFLRLREGRKNQSSAEPEKPASSLPSSPPLPPQLLMRKLVLGLAE<ELFL

Parental  WDPEESSFLVVRLRGPSGAGEEPSLSQYQRLLCINPPLFEIYQVLLSPTQHHVAL-IGIKGLMILELPKR
          W..E.S.FLV.RLRGPS.AGEEPSLSQY.R.LCIN.PLFEIYQ.LLSP.QHHVA...GIKGL.ILELPKR
Retrocopy WGAEDSAFLVMRLRGPSCAGEEPSLSQYRRRLCINAPLFEIYQALLSPAQHHVAS>VGIKGL-ILELPKR

Parental  WGKNSEFEGGKSTVNCSTTPVAERFFTSSTSLTLKHAAWYPSEMLEPHIVLLTSDNVIRIYSLREPQTPT
          WGKNSEFEGGKS.VNCSTTPVAERFFTSSTSLTLKH.AWYP.E.L...IV.LTSDNVIRIY....P...T
Retrocopy WGKNSEFEGGKSAVNCSTTPVAERFFTSSTSLTLKHVAWYPRELLDTQIVPLTSDNVIRIY----PLRMT

Parental  KVIVLSEAEEESLILNKGRAYTASLGETAVAFDFGPLSAVPKHIFGQKGKEEVAA-YPLYILYENGETFL
          KVIVLSEAEEESLILNKGRAYTASL.ETAVAFDFGPLSAVPKHIFG.KGKEEV.A.Y.LYILYEN.ETFL
Retrocopy KVIVLSEAEEESLILNKGRAYTASLEETAVAFDFGPLSAVPKHIFG*KGKEEVVA<YSLYILYENEETFL

Parental  TYISLLHSPGSVGKLLGPLPMHPAAEDNYGYDACAVLCLPCVPNILVIATESGMLYHCVVLEGEEEDDQT
          T..SLLHSPGSVGKL.GPLPMHPA.EDNYGY.ACAVLCLPCV.NILVI.TESGML..CVVLEGEEEDD.T
Retrocopy TFVSLLHSPGSVGKLFGPLPMHPAVEDNYGYHACAVLCLPCVANILVITTESGMLHYCVVLEGEEEDDHT

Parental  SEKSWDSRADLIPSLYVFECVELELALKLASGEDEPFDSDFSCPIKLHRDPKCPSRYHCTHEAGVHSVGL
          SEKSWDSRADLIPSLYVFECVELELALKLASGEDEPFDSDFSCP.KLHRDPKCP.R.H.TH.A.VHSVGL
Retrocopy SEKSWDSRADLIPSLYVFECVELELALKLASGEDEPFDSDFSCPLKLHRDPKCPLRFHYTH*AAVHSVGL

Parental  TWIHKLHKFLGSDEEDKDSLQELATEQKCFVEHILCTKPLPCRQPAPIRG-FWIVPDILGPTMICITSTY
          .WIHKLHKFLGSDEEDKDSLQELATEQKCFV.HILC.KPLPC.QPAP..G..WI.PDILGPT.ICITSTY
Retrocopy PWIHKLHKFLGSDEEDKDSLQELATEQKCFVQHILCRKPLPCSQPAPFQG<IWIIPDILGPTVICITSTY

Parental  ECLIRPLLSTVHPASPPLLCTREDVEVAESPLRILAETPDSFEKHIRSI-LQRSVANPAFLKSSEKDMAP
          E.L.RPLLSTVH.ASPPLLCTREDVE.AESPLRILAETPDSFEKHIRSI.LQR.VANPAFLKSSEKD.AP
Retrocopy EYLLRPLLSTVHLASPPLLCTREDVEMAESPLRILAETPDSFEKHIRSI<LQRGVANPAFLKSSEKDTAP

Parental  PPEECLQLISRATQVFREQYILKQDLAKEEIQRRVKLLCD-QKKKQLEDLNYCREERKSLREMAERLADK
          PP.ECLQLISRAT.VFR..YILKQD.A.EEIQ.RVKLLCD..KKKQLEDLNYC.EERKSLREMAERLADK
Retrocopy PPKECLQLISRATHVFRKYYILKQDPANEEIQWRVKLLCD<LKKKQLEDLNYCCEERKSLREMAERLADK

Parental  YEEAKEKQEDIMNRMKKVLHSFHSQLPVLSDSERDMKKEL-QLIPDQLRHLGNAIKQVTMKKDYQQRKME
          YEEAKEKQEDIMNRMKKVLHSF.SQLPVLSDSERD.KKEL...IP.QL.HLGNA.K.VTMKKDYQQRKME
Retrocopy YEEAKEKQEDIMNRMKKVLHSFQSQLPVLSDSERDTKKEL<IAIPHQLQHLGNAVKWVTMKKDYQQRKME

Parental  KVLSPQKPTITLSAYQRKCIQSILKEEGEHIREMVKQINDIRNHVNF
          KVLSPQKPTITLS.YQ.KCIQSILKE.GEHIREMVKQIN.I.NHVNF
Retrocopy KVLSPQKPTITLSTYQWKCIQSILKEKGEHIREMVKQINGI*NHVNF

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	26.68 RPM
ERP005899_muscle	0.05 RPM	22.33 RPM
SRP017611_brain	0.05 RPM	26.45 RPM
SRP017611_kidney	0.00 RPM	35.15 RPM
SRP017611_liver	0.00 RPM	21.97 RPM
SRP030211_testis	7.33 RPM	42.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1000 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1000 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	ENSBTAG00000011507	1 retrocopy	retro_btau_1000 ,
Myotis lucifugus	ENSMLUG00000014421	1 retrocopy	retro_mluc_2511,