RetrogeneDB ID: retro_pvam_535

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3647:85631..86547(+)
• Located in intron of: ENSPVAG00000011993

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSPVAG00000016570
• Aliases: None
• Description: calponin 2 [Source:HGNC Symbol;Acc:2156]

Sequence

>retro_pvam_535
ATGAACTCCACACAGTTCAATAAGGGGCCCTTGTAGAGGCTTTTGGCTGAGGTCATGAACCGGCTCCTGTCCAAATACGA
CCCTCAGAAGGAGGCAGAACTCCACAGCTGAATAGAGGGATTCACGGGCCTGTCTATCAGGCCCAAATTCCAGAAGGATG
GGATTACCCTGTGCACACTCATGAATAAGCTGTAGCCAGGCTTGGTCCCCAAGATAAACTGCTCCATGCAGAGCTGGCAC
CAGCTAGAAAACCTCTCCGATTTCATCAAGGCCATGGTCAGCTACGACAGGAACCCCACAGACCTGTTTGAGGTCGACAA
CCTGTTTGAGAGTGGGAACATGACACAGATGCAGGTGTCTTTTCTGCCCTGGTGGGGAAGGCCAAGACAAAGGGGCTGTA
GAGGGGCATGGACATTGGTATTAAGTACTCAGAGAGGCAAGAGTGGAACTTCGATGATGCCACAGTGAAGGCGGGCCAGT
ATGTCATCGGGCTCCAGATGGGCACCAGTAAGTGTGCCAGACAGTCTGGCATGATGGCGTACGGCAAGAGAAGGCCTCTG
TATGACCCGAAGAACCATATCCTGCCACCCATGGACCACTCGACCATCAGCCTGCAAATGGGCACCAACAAGTGTGCCAG
CCAGGTGGGCATGACACCTCCCAGGACCCAGCAGAACATCTATGAAACTAAGCTGAGGACTGACAAGTGTGACAACTCCT
CCATGTCTCTGCAGATGGGCTACATGCAGGGTGCCAAACTGAGCAGCCGGGTCTTTGGCCTGGGTGGGCAGATATACGAC
CCCAAGTACTGCCCGCAAGGCCCAGCAGCAGATGGGGCTCCGGGGGCTGCCAGTGACTGCCCAAGCCCAGGAGCAGCCCA
GAATAACCCTCTTACTACCATGAGAAGGCTAGCTAC

Alignment

ORF - retro_pvam_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRSWIEGLTGLSVGPDFQKGLKDGIILCTLMNKLQPG
          M.STQFNKGP...L.AEV.NRLLSKYDPQKEAEL.S.IEG.TGLS..P.FQ...KDGI.LCTLMNKL.PG
Retrocopy MNSTQFNKGPL*RLLAEVMNRLLSKYDPQKEAELHS*IEGFTGLSIRPKFQ---KDGITLCTLMNKL*PG

Parental  SVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLL-ALAGKAKTKGLHSG
          .VPKIN.SMQ.WHQLENLS.FIKAMVSY..NP.DLFE...LFESGNMTQ.QVS.L.AL.GKAKTKGL..G
Retrocopy LVPKINCSMQSWHQLENLSDFIKAMVSYDRNPTDLFEVDNLFESGNMTQMQVSFL<ALVGKAKTKGL*RG

Parental  VDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISLQ
          .DIG.KYSE.QE.NFDDAT.KAGQ.VIGLQMGT.KCA.QSGM.AYG.RR.LYDPKNHILPPMDHSTISLQ
Retrocopy MDIGIKYSERQEWNFDDATVKAGQYVIGLQMGTSKCARQSGMMAYGKRRPLYDPKNHILPPMDHSTISLQ

Parental  MGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGSV
          MGTNKCASQVGMT.P.T...IY.TKL.TDKCDNSSMSLQMGY.QGA..S..VFGLG.QIYDPKYCPQG..
Retrocopy MGTNKCASQVGMTPPRTQQNIYETKLRTDKCDNSSMSLQMGYMQGAKLSSRVFGLGGQIYDPKYCPQGPA

Parental  ADGASGAAGDCPSPGAA-PEYPPYYQEEDGY
          ADGA.GAA.DCPSPGAA.PE.P.YY.E...Y
Retrocopy ADGAPGAASDCPSPGAA<PE*PSYYHEKASY

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_535 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.

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Pteropus vampyrus	ENSPVAG00000016570	1 retrocopy	retro_pvam_535 ,