RetrogeneDB ID: retro_pvam_367

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2765:467838..468245(+)
• Located in intron of: ENSPVAG00000002506

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSPVAG00000012438
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_pvam_367
ATGAGCAAGTGGAATCAGGTATCATACGTGCAGCCAGTAGAGCTGGTGTTTCTAGCCCGCTTCAAGGAATGAGTTGGCTA
CAGACAACGGGGCCCAATGAAGAGACCAAGAGATTCCGGCCCCAGTTCTCAGATAAAGATGGTGATCACAGTGACAAAAA
AGTTGAACAGCACCAAGTGGTGGTTTTAAAAAAGGGAGACCCATCAGTTGAAGAAGCCATGAAAATTAAAGCAGAAATAA
AGGCTGCCAAAGCAGATGAAGAACCAGCTTCAGCTGATGGAAGAATCATGTATCGGAAACCAGTCAAGCGTTCCTCAGAT
GAAAAATATTCAGGTTTAGCAAGCTCAAAAAAGACAAATGAGGATGAAATAAGCAGGACTCAGCAAAAGCAAATAAAAAA
TAGTAGC

Alignment

ORF - retro_pvam_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 87.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKRNQVSYVRPAEPAFLARFKERVGYRE-GP-TVETKRIQPQLPDEDGDHSDKEDEQPQVVVLKKGDLS
          MSK.NQVSYV.P.E..FLARFKE.VGYR..GP...ETKR..PQ..D.DGDHSDK..EQ.QVVVLKKGD.S
Retrocopy MSKWNQVSYVQPVELVFLARFKE*VGYRQRGP<NEETKRFRPQFSDKDGDHSDKKVEQHQVVVLKKGDPS

Parental  AEEAMKIKAEIKAAKADEEPASADGRIMYRKPVKRSSDEKYSGLTASSKKKKTKEDEADEQDSVKKNS
          .EEAMKIKAEIKAAKADEEPASADGRIMYRKPVKRSSDEKYSGL.ASSKK....E.....Q...K..S
Retrocopy VEEAMKIKAEIKAAKADEEPASADGRIMYRKPVKRSSDEKYSGL-ASSKKTNEDEISRTQQKQIKNSS

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_367 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367 , retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307,