RetrogeneDB ID: retro_pvam_832

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_12954:21477..22111(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSPVAG00000001494
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A [Source:HGNC Symbol;Acc:11151]

Sequence

>retro_pvam_832
GTGGCAGTTCCCGAGACTCGCCTGGATCACACGATTTATGTCAACAGCCTCGAGGAGAAGATGAAGAAAGATGAGCTGAA
GAAGTCCTTGTACGCTATCTTCTCCCAGTTTGGCTAGATCCTGGACATCCCCCGGTGTCATGGAGCCTGGATGAGAGGTC
AGGCCTTTGTCCTCTTCCAAGTCAGCAGCACCACCAGTGTCCTGCACCCCACGCGGAGTTTCCCTTTCTATGGCAAGCCC
ATGAGCATCCAGCAGGCCAAGACTGACTCAGATATCGTTACCAAGGTAAAGATCACCTTCCTGGAGTGAGATCGTAAGTG
AGACGAAGCCCAAGAGCCAGGAGACTCTTTCTGGCTGCCCAGAAGGCTGTGCAGGGCAGGACGTCCACCCCGGTGGTGAG
GGCCCTTCCAGGGCTTGTCGCGGGCCTGCCACGGATGACTCAGGCGCCCCGCATCGTGCACCACATTCTGGGCCAGCCTC
CCTAAATGCCACCCCTGGCGTGATCCTGCCTCCAGGCCTCCCACCTGGCCAGATCCCATCGGTGGCCATGCCCCCACAGC
AGCTTATGCTCGGCCAGATGCCACCTGCCCAGCCTCTTTTAGAAAACCCACAAAATCACATCTTGCTCCTCACC

Alignment

ORF - retro_pvam_832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.26 %
• Parental protein coverage: 75.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVPESRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR
          .AVPE.R..HTIY.N.L.EK.KKDELKKSLYAIFSQFG.ILDI.......MRGQAFV.F..VSS.T..L.
Retrocopy VAVPETRLDHTIYVNSLEEKMKKDELKKSLYAIFSQFG*ILDIPRCHGAWMRGQAFVLF-QVSSTTSVLH

Parental  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAAKKAVQGG-AAAPVVGAVPG
          ....FPFY.KPM.IQ.AKTDSDI..K.K.TF.E.DRK....................G....PVV.A.PG
Retrocopy PTRSFPFYGKPMSIQQAKTDSDIVTKVKITFLE*DRK*DEAQEPGDSFWLPRRLCRAG<TSTPVVRALPG

Parental  PVPGMPPMTQAPRIMHHIPGQPPYMPP-PGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNH
          .V.G.P.MTQAPRI.HHI.GQPP.MPP.PG.I.PPGL.PGQIP..AMPPQQLM.GQMPPAQPL.ENP.NH
Retrocopy LVAGLPRMTQAPRIVHHILGQPP*MPP<PGVILPPGLPPGQIPSVAMPPQQLMLGQMPPAQPLLENPQNH

Parental  ILFLT
          IL.LT
Retrocopy ILLLT

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_832 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832 ,