RetrogeneDB ID: retro_btau_453

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:91304592..91305622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX7
• Ensembl ID: ENSBTAG00000031461
• Aliases: None
• Description: sorting nexin-7 [Source:RefSeq peptide;Acc:NP_001157409]

Sequence

>retro_btau_453
CTGATGCCGACATCCCCTTTATCAATGATAAACCAAGTCAAGTTTGAAGATGAGCCAGATTTGAAGGCTCTTTTTATTAC
AGTCGATGAACCTGAAAGCCATGTTACTACAATTGAAACTTTTATTACTTACAGGATTATTACTAAGACATCTCCTGGGG
AATTTGACTCCAGTGAATTTGAAGTTAGGAGACGTTATCAAGATTTCTTTTGGTTGAAAGAAAAACTTGAAGAAGCACAC
CCGACTCTGATTATTCCACCATTGCCAGAAAAGTTTATAGTGAAAAGAATGGTGGAACACGTTAATGAGGACTTCATTGA
GACACGCAGGAAGGCATTGCACAAATTTTTGAACCGAATTGCTGATCATTGAACTCTAACATTGAATGAAGATTTTAAAA
TTTTTCTTACTGCACAAGCTTGGGAACTGTCTTCTCAGAAGCAGCAAGGGCCTGGATTACTCAGCAGGATGGCACAGACA
GTCAAAGCGGTTGCATTGTCAATGAGAGGAGTTAAAAGTCGCCCCGAGGAGTTCATGGAAATGAATAACTACATTGAAAT
ATTTAGCCAGAAAACAAATTTGATAGATAAAATATCTCAGAGAATCTACAAGGAAGAACGGGAATATTTAGAGGAAATGA
AAGAATATGGCCCAATTTATATTCTTTCGGCATCGGAAGAAGATCTGGCTGATACTCTAAAAAGTGTTGCCAGCTGCATT
GACAAATGCTGTAAGGCCACTGAAAAATGGACGTCTGGACTCTCAGAGGCCCTGCTTCCTGTCGTACAAGAGTATGTGCT
TTATAGTGAAATGTTAATGGCTGTCATGAAAAGAAGAGACCAAATACAGGCAGACCTGGATTCCAAAGTTGAAGCTTTGA
CGTCCAAAAAGGCAATATACTGATCCGCTTATGGAAGAGATTGGAAAACTGTAAGATAAAGTGGAGTGTGCTGATAATGC
CCTGAAAGCAGATTGGGAAAGATGGAAACAAAGCATGCAAAATGATATCAAGTCAGCATTTACAAAAATA

Alignment

ORF - retro_btau_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 76.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMPTSPLSMINQVKFEDEPDLKDLFITVDEPESHVTTIETFITYRIITKTSRGEFDSSEFEVRRRYQDFL
          LMPTSPLSMINQVKFEDEPDLK.LFITVDEPESHVTTIETFITYRIITKTS.GEFDSSEFEVRRRYQDF.
Retrocopy LMPTSPLSMINQVKFEDEPDLKALFITVDEPESHVTTIETFITYRIITKTSPGEFDSSEFEVRRRYQDFF

Parental  WLKEKLEEAHPTLIIPPLPEKFIVKGMVERFNDDFIETRRKALHKFLNRIADHPTLTFNEDFKIFLTAQA
          WLKEKLEEAHPTLIIPPLPEKFIVK.MVE..N.DFIETRRKALHKFLNRIADH.TLT.NEDFKIFLTAQA
Retrocopy WLKEKLEEAHPTLIIPPLPEKFIVKRMVEHVNEDFIETRRKALHKFLNRIADH*TLTLNEDFKIFLTAQA

Parental  SEFSSHKKQGPGLLSRMGQSVRAVALSMRGVKSRPEEFMEMNNFIEIFSQKINLIDKISQRIYKEEREYL
          .E.SS.K.QGPGLLSRM.Q.V.AVALSMRGVKSRPEEFMEMNN.IEIFSQK.NLIDKISQRIYKEEREYL
Retrocopy WELSSQKQQGPGLLSRMAQTVKAVALSMRGVKSRPEEFMEMNNYIEIFSQKTNLIDKISQRIYKEEREYL

Parental  DEMKEYGPIHILWSASEEDLADTLKSVASCIDKCCKATEKRMSGFSEALLPVVHEYVLYSEMLMAVMKRR
          .EMKEYGPI.IL.SASEEDLADTLKSVASCIDKCCKATEK..SG.SEALLPVV.EYVLYSEMLMAVMKRR
Retrocopy EEMKEYGPIYIL-SASEEDLADTLKSVASCIDKCCKATEKWTSGLSEALLPVVQEYVLYSEMLMAVMKRR

Parental  DQIQAELDSKVEALTSKKA-DTDLLTEEIGKLEDKVECANNALKADWERWKQNMQNDIKSAFTNM
          DQIQA.LDSKVEALTSKKA..TD.L.EEIGKL.DKVECA.NALKADWERWKQ.MQNDIKSAFT..
Retrocopy DQIQADLDSKVEALTSKKA>YTDPLMEEIGKL*DKVECADNALKADWERWKQSMQNDIKSAFTKI

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	22.13 RPM
ERP005899_muscle	0.00 RPM	8.60 RPM
SRP017611_brain	0.00 RPM	1.69 RPM
SRP017611_kidney	0.06 RPM	11.20 RPM
SRP017611_liver	0.00 RPM	11.40 RPM
SRP030211_testis	0.00 RPM	1.44 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_453 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031461	1 retrocopy	retro_btau_453 ,
Choloepus hoffmanni	ENSCHOG00000008131	2 retrocopies	retro_chof_1097, retro_chof_1388,
Gorilla gorilla	ENSGGOG00000023577	1 retrocopy	retro_ggor_744,
Macropus eugenii	ENSMEUG00000011320	1 retrocopy	retro_meug_1016,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420,
Tupaia belangeri	ENSTBEG00000000168	1 retrocopy	retro_tbel_2595,