RetrogeneDB ID: retro_pvam_679

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_657:21085..21990(-)
• Located in intron of: ENSPVAG00000006815

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIPK2
• Ensembl ID: ENSPVAG00000003017
• Aliases: None
• Description: receptor-interacting serine-threonine kinase 2 [Source:HGNC Symbol;Acc:10020]

Sequence

>retro_pvam_679
GAATATATGCCAAATGGATCATTAAATAAACTCCTATATAGGAAAACTGAATATCCTGATGTTGCCTTCCATTGAGATTC
TGCATGCTTCATGAAATTGCACTGGGTATAAATTATCTGCACAATATGACTTCTCCTCTACTTCATCATGACTTGAAGAC
TCAAAATATCTTATTGGATAATGAATTTCATGTTAAGATTGCAGATTTTGGTTTATCAAAATGGCACATGATGTCCCTGT
CGAAATCATGAAGTTGTAAATCTCCACCAGAAGGAGGGACAATTATCTATATGCCATCTGAAAACTATGAATGTTGACAA
ATATCAAGAGTCAGTGTTAAGCATGGTATATATAGCTATGCAGTTATCGCATAGGAAGTCTCATCCAGAAAACAGCCTTT
TGAGGAAGTCACCAATCTTTTGCAGATTATGTACAGTGTGTCACAAGGCCATCGACATGACATTAGTGAAGAAAGATTGT
CATTTGATATACCTCAGTGAGCACTGATCTCTCTCACAGAAGGCAGATGGACACAAAATCTAGATAAAAAGCTGTCCTTC
TTAAAACGTTTAATAAAACTTGAACCAGTCCCGAGAACACTTGAAGAGATAACTTTACTTGATGTTATACAACTAAAAAA
AACAAAGTTACAGAGCACTTCAAGCACTATTTATATATGTGACAAGAAGAAAACAGAGCAATCTCTGGATGTGTCTCTAA
ATCATGGTCCACAGAAGGAATTATGTGGATCCTCTCAGCTCCAAAAAAGTAGTGGTTCTCCTGGAACCTCAAGGTCCCTG
TCAGCTCCTCAAGACAATGATTTTTTTATCCAGAAAACTCAGGACTTCTCTATGCTGCACCACCATCCAGTAAATCACAG
TTGGGATGGCAACGTGTCTGGCTCA

Alignment

ORF - retro_pvam_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 56.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYMPNGSLNELLHRKTEYPEVAW-PLRFRILHEIALGVNYLHNMNPPLLHHDLKTQNILLDNEFHVKIAD
          EYMPNGSLN.LL.RKTEYP.VA..PLRF..LHEIALG.NYLHNM..PLLHHDLKTQNILLDNEFHVKIAD
Retrocopy EYMPNGSLNKLLYRKTEYPDVAF<PLRFCMLHEIALGINYLHNMTSPLLHHDLKTQNILLDNEFHVKIAD

Parental  FGLSKWRLMSLSQSRSSKSAPEGGTIIYMPPENYEPGQKSRASVKHDIYSYAVIMWEVLSRKQPFEEVTN
          FGLSKW..MSLS.S.S.KS.PEGGTIIYMP.ENYE..Q.SR.SVKH.IYSYAVI..EV.SRKQPFEEVTN
Retrocopy FGLSKWHMMSLSKS*SCKSPPEGGTIIYMPSENYEC*QISRVSVKHGIYSYAVIA*EVSSRKQPFEEVTN

Parental  PLQIMYSVSQGHRPDTSEESLPFDIPHRAVMLDLIKAGWAQNPDERPSFLKCLIELEPVLRTFEEITFFE
          .LQIMYSVSQGHR.D.SEE.L.FDIP..A....L....W.QN.D...SFLK.LI.LEPV.RT.EEIT...
Retrocopy LLQIMYSVSQGHRHDISEERLSFDIPQ*A-LISLTEGRWTQNLDKKLSFLKRLIKLEPVPRTLEEITLLD

Parental  AVMQLKKTKXXXXXXXXXXHDKKTELSLSVSLNHG-QEESCGSLQPPKSGGSPGTSRSLSAPQDNEPSSR
          .....................KKTE.SL.VSLNHG.Q.E.CGS.Q..KS.GSPGTSRSLSAPQDN.....
Retrocopy VIQXXXXKLQSTSSTIYICDKKKTEQSLDVSLNHGPQKELCGSSQLQKSSGSPGTSRSLSAPQDNDFFIQ

Parental  KSQDF-MQHHHPANHSWDSNMSAA
          K.QDF.M.HHHP.NHSWD.N.S..
Retrocopy KTQDFSMLHHHPVNHSWDGNVSGS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_679 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000010960	1 retrocopy	retro_mputfur_1603,
Pteropus vampyrus	ENSPVAG00000003017	1 retrocopy	retro_pvam_679 ,