RetrogeneDB ID: retro_pvam_988

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_21104:9593..10135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM248
• Ensembl ID: ENSPVAG00000002978
• Aliases: None
• Description: transmembrane protein 248 [Source:HGNC Symbol;Acc:25476]

Sequence

>retro_pvam_988
TTCTTTGTCCTCGGGTTATTTCTTAAAATCAAGGAGATTAAGCTGCCAGAAAGGGCAAAGAATTAGAATACTTTTCTGTG
GTGGGTTAATGATTTGGATGTGTGTGTATCAAAGAATGAAACATTAAAGCATCTCACAAATGATACCACAACTCTGGAAA
GCACAATGACCAGCAGGCAGGCCAGAGTGTAACCCCAGTCCCCACAGGCTGTGGAGGACTCAGGCCCTGTTAACACCACA
GTTGCAATTGCCTTTACTTTGGACCCACTCAAACCCTTTGAAGGGTACTCTCACAATGTCACTCATCTGTACTTGACCAT
GTTAGGGCATCAGATTGAACTTTCAGACATAGAAGCCTTTGAGGAGATAAATATTACCTTTACCCTGCCTGCAGCTTGCG
CTTAGATGCCTGTGCCCTTCACAATCACTGTGTACAGGGACAGTTCACATCCTGCATGACCCTCACAGCCAACCCCAGTG
TGTCCCCCATCACTGTACAGCCACCACACTGTGTTACTGACACATAGAGCAATGTCATGCTC

Alignment

ORF - retro_pvam_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLTLGYFFK-KEIKSPEMAEDWNTFLLRFNDLDLCVSENETLKHLTNDTTTPESTMTSGQARLSTQSPQA
          F..LG.F.K.KEIK.PE.A...NTFL...NDLD.CVS.NETLKHLTNDTTT.ESTMTS.QAR...QSPQA
Retrocopy FFVLGLFLKIKEIKLPERAKN*NTFLWWVNDLDVCVSKNETLKHLTNDTTTLESTMTSRQARV*PQSPQA

Parental  LEDSGPVNISVAITLTLDPLKPFGGYSRNVTHLYSTILAHQIGLSGREAHEEINITFTLPAAWS-SDDCA
          .EDSGPVN..VAI..TLDPLKPF.GYS.NVTHLY.T.L.HQI.LS..EA.EEINITFTLPAA....D.CA
Retrocopy VEDSGPVNTTVAIAFTLDPLKPFEGYSHNVTHLYLTMLGHQIELSDIEAFEEINITFTLPAACA<LDACA

Parental  LHGHCEQVVFTACMTLTANPGVFPVTVQPPHCVPDTYSNATL
          LH.HC.Q..FT.CMTLTANP.V.P.TVQPPHCV.DT.SN..L
Retrocopy LHNHCVQGQFTSCMTLTANPSVSPITVQPPHCVTDT*SNVML

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_988 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988 , retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,