RetrogeneDB ID: retro_pvam_732

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_10125:56579..57246(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSPVAG00000009190
• Aliases: None
• Description: nucleosome assembly protein 1-like 4 [Source:HGNC Symbol;Acc:7640]

Sequence

>retro_pvam_732
ACAGTCTCCTATGCTCCTTCGAGTTACATCAATACTTTACCTAAAGCAGTAAAGAGAAGAATCGATGCATTGAAACAACT
TCAGGGGAAGTGTGGTCACACACAAGCCAAGTTCTATGACGAGGTCCATGACCTGAAGAGGAAGTACATGGCACTGTATC
AGCCTCTCTTTGATAAGAGAAGGGGATTCGTCACTGACGATGTTGAGCTGACAGATGCAGAATCGGAATGGCACAGTGAG
AATGAAGAGGAGAATAAATTGGCTGGAGACGTGAAACATAAGTCATAGCAGAAAAAGAAGGCACAAAGCAAAAGAACCAA
GTCCCAGAGGGATTGCGGGCTTCTGGTTCACCATCTTCAGAAATGTATATATGCTACGTGACTTAGTCCAGGAATATGAT
GAGTCAATCTTGAAACACCTGCAGGGTATTAAAGTGAAAATTTCCAACCCTGGACAGCCTCTGTCTTTTGTATTATGGTT
CCACTTTGAACCCAATGACTACTTTACCAATTCAGTCCTGACAAAAATGGTACAAGGTGAAGTCGGAGCGAGATAAGGCC
CCTTTTCCTTTGAAGTTCCTGAAATACTCGAATGTGATGACTGCACTAGTGACTGGAAGAAAGGGAAAAAAATGCCACAG
TCAAAATGATCAAGAAAAAGCAGAAAC

Alignment

ORF - retro_pvam_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.0 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVAHTPSSYIETLPTAVKRRINALKQLQVKCAHIEAKFYEEVHGLERKYAALYQPLFDKRREFVTGDVEP
          .V...PSSYI.TLP.AVKRRI.ALKQLQ.KC.H..AKFY.EVH.L.RKY.ALYQPLFDKRR.FVT.DVE.
Retrocopy TVSYAPSSYINTLPKAVKRRIDALKQLQGKCGHTQAKFYDEVHDLKRKYMALYQPLFDKRRGFVTDDVEL

Parental  TDAESEWHSENEEEDKLAGDMKNK-VVIAEKEATQAEEPNPKGI-PGFWFTIFRNVDMLSELVQEYDEPI
          TDAESEWHSENEEE.KLAGD.K.K.V........Q.....P.G...GFWFTIFRNV.ML..LVQEYDE.I
Retrocopy TDAESEWHSENEEENKLAGDVKHK<VIAEKEGTKQKNQV-PEGL<AGFWFTIFRNVYMLRDLVQEYDESI

Parental  LKHLQDIKVKFSEPGQPMSFVLEFHFEPNDYFTNSVLTKT-YKMKSEPDKADPF-SFEGPEIVDCDGCTI
          LKHLQ.IKVK.S.PGQP.SFVL.FHFEPNDYFTNSVLTK..YK.KSE.DKA.PF.SFE.PEI..CD.CT.
Retrocopy LKHLQGIKVKISNPGQPLSFVLWFHFEPNDYFTNSVLTKM>YKVKSERDKA-PF<SFEVPEILECDDCTS

Parental  DWKKGKNVTVKTIKKKQKH
          DWKKGK.........K...
Retrocopy DWKKGKKMPQSK*SRKSRN

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_732 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000009190	1 retrocopy	retro_pvam_732 ,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282, retro_pvam_306,