RetrogeneDB ID: retro_pvam_694

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_749:394325..395102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000010989
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP62CL
• Ensembl ID: ENSPVAG00000001787
• Aliases: None
• Description: nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960]

Sequence

>retro_pvam_694
AGCTTAAAGGCCCCTGGAGCAGCCCCTCCCTCATCCATAGCAACGTCCACTGCCGCCCCCACCACGACCAGCAGCAGCTT
CGCTCTGAATCTGAAACCCCTGGCTCCAGCCGGGGTGTCCAGCACTGCGCCCACCGCCGTGACTGCTCCGTCTGGCCCCA
GTGTGGCCACCGGGGTGTCCACCAGTCCTGCGATGACCTATGCCCAGCTGGAGAGTCTGATCAACAAGTGGAGCCTGGAG
CTGGAGGACCAGGAGCGACACTTCCTCCAGCAGGCCACGCAGGTCAACGCCTGGGACCGCACACTCATCGAGAACGGGGA
GAAGATCACCACCCTGCACCGCGAGGTGGAGAAGGTGAAGCTGGACCAGAAGAGGCTGGACCAGGAGCTGGACTTCATCC
TGTCCCAGCAGAAGGAGCTGGAAGACCTGCTCAGCCCGCTGGAGGAGTCGGTCAAGGAGCAGAGCGGGACCGTGCACCTG
CAGCACGCCGACGAGGAGCGCGAGAAGACCTACAAGCTGGCCGAGAACATCGACGCGCAGCTGAAGCGCATGGCGCAGGA
CCTCAAGGACATCATCGAGCACCTGAACACGTCCGGGGGCCCCGCCGACACCAGCGACCCCCTGCAGCAGATCTGCAAGA
TCCTCAACGCGCACATGGACTCGCTGCAGTGGGTCGACCAGAACTCGGCCCTGCTGCAGAGGAAGGTGGAGGAGGTGAGC
AGGGTGTGCGAGGGGCGGCGCAAGGAGCAGGAGCGCGGCTTCCGCATCACGTTCGAC

Alignment

ORF - retro_pvam_694 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.0 %
• Parental protein coverage: 95.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STAATGLSSTTSTTTTTTV-TTTTTTTTTTTSGLAFSLKPLTSPGINNSIPFTSTVNAIVT-PVMTYGHL
          S..A.G.....S..T.T...TTT..........LA......T.P.........S......T.P.MTY..L
Retrocopy SLKAPGAAPPSSIATSTAAPTTTSSSFALNLKPLAPAGVSSTAPTAVTAPSGPSVATGVSTSPAMTYAQL

Parental  EDLVNKWSLELEDQE-YFIHKATQVNDWDYTLNENAEKITTLYRKVEKAKLDQKRLEQELDFVLSQQNEL
          E.L.NKWSLELEDQE..F...ATQVN.WD.TL.EN.EKITTL.R.VEK.KLDQKRL.QELDF.LSQQ.EL
Retrocopy ESLINKWSLELEDQERHFLQQATQVNAWDRTLIENGEKITTLHREVEKVKLDQKRLDQELDFILSQQKEL

Parental  ENLLTPLVVTMKGHRGSVYQQHEDEDCERIYKLAENVDAQLKRMTQELRGIIEHLNIFGRLANTTGPFQQ
          E.LL.PL....K...G.V..QH.DE..E..YKLAEN.DAQLKRM.Q.L..IIEHLN..G..A.T..P.QQ
Retrocopy EDLLSPLEESVKEQSGTVHLQHADEEREKTYKLAENIDAQLKRMAQDLKDIIEHLNTSGGPADTSDPLQQ

Parental  ICKILSAHLDSLQWIIQNSGMLQRKIEEVTQVFKDLHCKEQEHNMSIAFD
          ICKIL.AH.DSLQW..QNS..LQRK.EEV..V......KEQE....I.FD
Retrocopy ICKILNAHMDSLQWVDQNSALLQRKVEEVSRVCEGRR-KEQERGFRITFD

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_694 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017963	1 retrocopy	retro_cfam_218,
Dasypus novemcinctus	ENSDNOG00000001467	1 retrocopy	retro_dnov_1108,
Felis catus	ENSFCAG00000001984	1 retrocopy	retro_fcat_120,
Macropus eugenii	ENSMEUG00000001005	1 retrocopy	retro_meug_1130,
Nomascus leucogenys	ENSNLEG00000013865	1 retrocopy	retro_nleu_2076,
Pteropus vampyrus	ENSPVAG00000001787	1 retrocopy	retro_pvam_694 ,
Vicugna pacos	ENSVPAG00000003649	1 retrocopy	retro_vpac_448,