RetrogeneDB ID: retro_pvam_378

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2841:304808..305559(-)
• Located in intron of: ENSPVAG00000000768

Retrocopy information

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

Parental gene information

• Parental gene symbol: BBS4
• Ensembl ID: ENSPVAG00000015883
• Aliases: None
• Description: Bardet-Biedl syndrome 4 [Source:HGNC Symbol;Acc:969]

Sequence

>retro_pvam_378
ACTTTAGGATTACTCTACTTACAGCTCGGCATTTAACAGAAGGCATTTGAAAATCTTGAGAATGTAATGACTTATGACCC
TACCAACTATAAGGCCATTTTGGCAGCAGGCAGCATGATGCAGACCCACAGAGACTTTGATGTCGCCCTCACCAAATACA
GAGTTGTAGGTTGTGCTGTTCCAGAGAGTCTTCCACTCTGGAATTACATTGGAATGTGTTTCTTGGAAAGAAGAAATATG
TAGCTGCTATCGGCTGCCTGAAATGAGCCAACTACTTGGCACCCATCGATTGGAAGATTCTCTATTATTTGGGCCTTGTC
CACTTGACCATGCAGCGGTATGCATCAGCTTTCCACTTTCTCAGTGCAGCCATCAACTTCCAGCCAAAGATGGGGGAGCT
CTACATGCTCTTGGCTGTGGCTCTGACCAATCTGGAAGATACAGAAAATGCCAAGAGAGCCTATGCAGAAGCTGTCCACC
TGGATAAGTGTAATCCTTTAGTCAACCTGAACTACGCTGTGCTGCTGTACAACCAAGGTGAGAAGCGGGGACCCTGGCCC
AATATCAGGAGATGGAGAAGAAAGTCAACCTACTCAAGGAGAGTAGCTTTCTGGAATTTCACTCTGAGATGGTGGAGATG
GCCCAGAAGTTGGGAGCTGCTCTCCAGGTTGGAGAGGCACTGGTCTGGACTAAACCAGTTAAAGATCCCAAATCAAAGCA
CTGGACCACTTCAGCAAAGCTGCCAGTTTCC

Alignment

ORF - retro_pvam_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 50.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLGLLYLQLGIYQKAFEHLGNALTYDPTNYKAILAAGSMMQTHGDFDVALTKYRVVACAVPESPPLWNNI
          TLGLLYLQLGI.QKAFE.L.N..TYDPTNYKAILAAGSMMQTH.DFDVALTKYRVV.CAVPES.PLWN.I
Retrocopy TLGLLYLQLGI*QKAFENLENVMTYDPTNYKAILAAGSMMQTHRDFDVALTKYRVVGCAVPESLPLWNYI

Parental  GMCFF-GKKKYVAAISCLKRANYLAPFDWKILYNLGLVHLTMQQYASAFHFLSAAINFQPKMGELYMLLA
          GMCF..GKKKYVAAI.CLK.ANYLAP.DWKILY.LGLVHLTMQ.YASAFHFLSAAINFQPKMGELYMLLA
Retrocopy GMCFL<GKKKYVAAIGCLK*ANYLAPIDWKILYYLGLVHLTMQRYASAFHFLSAAINFQPKMGELYMLLA

Parental  VALTNLEDTENAKRAYAEAVRLDKCNPLVNLNYAVLLYNQGEKQ-GALAQYQEMEKKVNLLKDSSSLEFD
          VALTNLEDTENAKRAYAEAV.LDKCNPLVNLNYAVLLYNQGEK..G.LAQYQEMEKKVNLLK.SS.LEF.
Retrocopy VALTNLEDTENAKRAYAEAVHLDKCNPLVNLNYAVLLYNQGEKR<GTLAQYQEMEKKVNLLKESSFLEFH

Parental  SEMVEMAQKLGAALQVGEALVWTKPGKDPKSKHRTTSTSKAAS
          SEMVEMAQKLGAALQVGEALVWTKP.KDPKSKH.TTS.....S
Retrocopy SEMVEMAQKLGAALQVGEALVWTKPVKDPKSKHWTTSAKLPVS

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_378 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
Nomascus leucogenys	ENSNLEG00000014060	1 retrocopy	retro_nleu_2549,
Pteropus vampyrus	ENSPVAG00000015883	1 retrocopy	retro_pvam_378 ,