RetrogeneDB ID: retro_pvam_144

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1609:261681..262524(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000002070
• Aliases: None
• Description: None

Sequence

>retro_pvam_144
GTGACCAGGCTTCTGGGCACGGTGCAGAGAGTTGCTTTGGCAGCTGCGCACTGCCGTTGCGGCCGCGGGGCCTGTTCTAT
GCTGTGAGGAGTGGCCGCGAGGCCCGGGTCTTCCTGACCTGGAATTAGCGTAGAGCACAGGTGGACCGATTTCCTGCTGC
CAGATTTAAGAAGTTAGCCACAGAAGAGGAAGCCTGGGCCTTTGTCAGAAACTTTGGGAGCCCTGATGGTTCAGAAGGGC
AGAAAGATAAACAGGTATAAGAATCACAAGTGAAAGTCAACAAGCAACTCTGTGAGCCCCTGGCTGAAGGAAATGAGAAC
TCAGAGCCATGTGCAAAGCATGTAAAATGGAACACTGAGGCAACACCTTTGGTTGGCAAGAACACGGCCTCTTATATGAG
AGACTACGCCGTTGTCTACACTGGTGACTGCTGCTCCAGTAACACACAGAGGAAGGCACAAGCAGGAATCGGTGTTTACT
GGGGGCCTGGCCACCCTTTAAACATAGGCATTAGACTTCCTGGGCAACAAACGAACCAAAGAGCAGAAATTCATGTGGCC
TGCAAAGCCATCCCACAAGCAAGGGCGCAAAACATCAGTAAGTTGGCTCTATATACGGACAGTATGTTTTACGATCAATG
GTATTGCTGACTGAGTTCGAGGTTGGAAGTAAAACAGATGGAGAATAAGCAGTGGGAAAAAGGTGATCAACAAATAGAAC
TTCTTAGAGCTACAGAAACTTGCTCAGGGCATGGACATTCAGAGGATGTGTGTTCCTGATCATTTGGGATTTGTAGGCAA
TGAAACAGCTGACAGATTAGCAAAAGGAGCAAAGCAATCCCAA

Alignment

ORF - retro_pvam_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTRLLGVARRVALAAVRRGCGCGA-LGMFYAVRRGRRAGVFLTWSECRAQVDRFPAARFKKFATEEEAWA
          .TRLLG...RVALAA....C.CG...G.FYAVR.GR.A.VFLTW...RAQVDRFPAARFKK.ATEEEAWA
Retrocopy VTRLLGTVQRVALAAAH--CRCGR<RGLFYAVRSGREARVFLTWN*RRAQVDRFPAARFKKLATEEEAWA

Parental  FVRNSGSPGGAEGQKDEPVQESEAKGSKRLREPPADGDEDSEPCAKLAKPRAGPAPPVGKDTFSYMGEHA
          FVRN.GSP.G.EGQKD..V.ES..K..K.L.EP.A.G.E.SEPCAK..K......P.VGK.T.SYM...A
Retrocopy FVRNFGSPDGSEGQKDKQV*ESQVKVNKQLCEPLAEGNENSEPCAKHVKWNTEATPLVGKNTASYMRDYA

Parental  IVYTDGCCSRNGRHRARAGIGVYWGPGHPLNISVRLPGRQTNQRAEIHAACKAIEQARAQRISKLALYTD
          .VYT..CCS.N....A.AGIGVYWGPGHPLNI..RLPG.QTNQRAEIH.ACKAI.QARAQ.ISKLALYTD
Retrocopy VVYTGDCCSSNTQRKAQAGIGVYWGPGHPLNIGIRLPGQQTNQRAEIHVACKAIPQARAQNISKLALYTD

Parental  SM-FTINGITNWVEGWKKNGWRTSTGKEVINKEDFAELERLAQGMDIQWMHIPGHSGFVGNEEADRLARL
          SM.FTINGI...V.GWK.N.WR.S.GK.VINK..F.EL..LAQGMDIQ.M..P.H.GFVGNE.ADRLA..
Retrocopy SM>FTINGIAD*VRGWK*NRWRISSGKKVINK*NFLELQKLAQGMDIQRMCVPDHLGFVGNETADRLAK-

Parental  GARQPE
          GA.Q..
Retrocopy GAKQSQ

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_144 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144 ,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,