RetrogeneDB ID: retro_pvam_1177

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3703:18199..19002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN2
• Ensembl ID: ENSPVAG00000005822
• Aliases: None
• Description: makorin ring finger protein 2 [Source:HGNC Symbol;Acc:7113]

Sequence

>retro_pvam_1177
ATGAGCACCAAGCAGATCACTTGCAGGTATTTTATACATAGTGTGTGTTGGGAAGGAAACCAATGCCTGTTTTCACATGA
CTTGGCAAACAGGAAGCCATCCACCATCTGCAAATGCTATCAGAAGTGTTGTTACGCCTATGGAACTTGTTGCAGATACG
ATCACACGAGGCCCTCTGGTGTGGCTGCTGGTGCTGTGGGCACTGTGCTGCACAGTGTGCCCTCCCTGAGTTTCCACAGT
CCTCACCCTCCTTCTGACCTCACTGCATCCATTGCGAAAACTAACTTATGTCAACCTGGGGAATGTGAAAAGAGGACATT
GGTACTTAGAGACTGAAATCTTTCTTCATTGGCTAAAGAAAAGGCTTCCCCAACTATGGTGAATAATCTAGGAAGTGGTA
GTGACTCCCAGAGTAGCCCAGAAATGAAGCCACATTCCTACCTACATGCAATCAGGAGTGGTCTTGATGACTGAGAAGCC
AGCAGCTCCTACGACAGTGTGCAGCAGCTATGCCCCTATGCAGATGCCAGAGAGTGCCAATTTGAAGATATTTGTGTCTA
CTTGCATGGAGAAGTGTGTGAAACCTGTAGGTTACAAGTCCTGCACCCCTTTGACCCAGAACAAAGAAAAGCTCATGAGA
AGATCTGCATGTCGACATTCAAACACGAGATGGGGAAGGCAAGTCAGGCAAGTCAGGACAAAGTGTGTAGTATCTGCATG
GAAGTGATCCTTGAGAAGGCATCTGCTTCTGAGAGGAGATTTGGGATTCTCTCCAATTGCAATCAACATACTGCTTGTCC
TGC

Alignment

ORF - retro_pvam_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 83.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTKQITCRYFMHGVCREGNQCLFSHDLANSKPSTICKYYQKGCCAYGTRCRYDHTRPPAAAGGAMGTVP
          MSTKQITCRYF.H.VC.EGNQCLFSHDLAN.KPSTICK.YQK.C.AYGT.CRYDHTRP...A.GA.GTV.
Retrocopy MSTKQITCRYFIHSVCWEGNQCLFSHDLANRKPSTICKCYQKCCYAYGTCCRYDHTRPSGVAAGAVGTVL

Parental  HSVPSPSFHSPHPPSDLTASIVKTNLHEPGKREKRTLVLRDRNLSGMAEEKASPTVVNNPGSGSDLQSSP
          HSVPS.SFHSPHPPSDLTASI.KTNL..PG..EKRTLVLRD.NLS..A.EKASPT.VNN.GSGSD.QSSP
Retrocopy HSVPSLSFHSPHPPSDLTASIAKTNLCQPGECEKRTLVLRD*NLSSLAKEKASPTMVNNLGSGSDSQSSP

Parental  EMKPHSYLDAIRSGLDDLEASSSYSSEQQLCPYAAAGECRFEDACVYLHGEVCEICRLRVLHPFDPEQRK
          EMKPHSYL.AIRSGLDD.EASSSY.S.QQLCPYA.A.EC.FED.CVYLHGEVCE.CRL.VLHPFDPEQRK
Retrocopy EMKPHSYLHAIRSGLDD*EASSSYDSVQQLCPYADARECQFEDICVYLHGEVCETCRLQVLHPFDPEQRK

Parental  AHEKICMSTFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNH-TYCLSC
          AHEKICMSTF.H..E..........KVCSICMEVILEKASASERRFGILSNCN..TYCLSC
Retrocopy AHEKICMSTFKH--EMGXXXXXXXXKVCSICMEVILEKASASERRFGILSNCNQ<TYCLSC

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_1177 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016733	1 retrocopy	retro_cjac_2362,
Mus musculus	ENSMUSG00000000439	2 retrocopies	retro_mmus_3578, retro_mmus_544,
Otolemur garnettii	ENSOGAG00000003255	1 retrocopy	retro_ogar_3196,
Pteropus vampyrus	ENSPVAG00000005822	1 retrocopy	retro_pvam_1177 ,