RetrogeneDB ID: retro_pvam_1140

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3194:99617..99905(+)
• Located in intron of: ENSPVAG00000014344

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf53
• Ensembl ID: ENSPVAG00000006321
• Aliases: None
• Description: chromosome 19 open reading frame 53 [Source:HGNC Symbol;Acc:24991]

Sequence

>retro_pvam_1140
GCACAGGCGCAGCACAAGTTCCAGACACACAAGCTGGAGAAGAGCCCAATGGCAGTGGCAGCTTCAGAACAGAACTGGGG
CCCGAGTAAGGGAGGTTGTGTTATAGCTCCCAAGAAGGCGCGCATTGTGCAGCAACGAAAGCTCAAGAAGGGCCTGGAGG
TTGGGATCCGGAAGATCAAACACGATGTGGTAATAAAAGCCAGCACCAGTATGCCCAAGAAGCTGGCGCTGCTGCAAGCC
CGCACCAGGACGGGGGCAGCTTCCGCCTCCTCCACCAAGACATCTTCC

Alignment

ORF - retro_pvam_1140 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 99.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQGQRKFQARKPVKSKTATVAASERNRGPRKGGRVIAPKKAHIVQQQKLKKDLEVGIRKKIEHDVVMKAS
          AQ.Q.KFQ..K..KS..A.VAASE.N.GP.KGG.VIAPKKA.IVQQ.KLKK.LEVGIR.KI.HDVV.KAS
Retrocopy AQAQHKFQTHKLEKSPMA-VAASEQNWGPSKGGCVIAPKKARIVQQRKLKKGLEVGIR-KIKHDVVIKAS

Parental  TSLPKKLALLKGPTKKREAASSSSTKTPS
          TS.PKKLALL...T....AAS.SSTKT.S
Retrocopy TSMPKKLALLQART-RTGAASASSTKTSS

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_1140 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002525	1 retrocopy	retro_btau_35,
Callithrix jacchus	ENSCJAG00000004427	3 retrocopies	retro_cjac_1003, retro_cjac_2634, retro_cjac_291,
Homo sapiens	ENSG00000104979	1 retrocopy	retro_hsap_628,
Gorilla gorilla	ENSGGOG00000027024	1 retrocopy	retro_ggor_550,
Monodelphis domestica	ENSMODG00000011876	2 retrocopies	retro_mdom_1436, retro_mdom_926,
Nomascus leucogenys	ENSNLEG00000013141	1 retrocopy	retro_nleu_452,
Otolemur garnettii	ENSOGAG00000007185	1 retrocopy	retro_ogar_640,
Procavia capensis	ENSPCAG00000014250	1 retrocopy	retro_pcap_26,
Pan troglodytes	ENSPTRG00000010565	1 retrocopy	retro_ptro_457,
Pteropus vampyrus	ENSPVAG00000006321	1 retrocopy	retro_pvam_1140 ,
Tursiops truncatus	ENSTTRG00000010354	1 retrocopy	retro_ttru_317,