RetrogeneDB ID: retro_pvam_1207

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_416:316738..317314(-)
• Located in intron of: ENSPVAG00000009187

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSPVAG00000003150
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_pvam_1207
TCTGGGGTCTCTATGTTGCTGTAAAGGGAAGAGCTCAAGGAGATCAAGGAGGAGACTGGCTTTCCTACTGTCAGATCACG
CACATCTATAGCCAGTTTGCCAATGTGGACAAAGTTGAAAAGGGGCTCTCAGCCAGGAAGATTTCCAGTGGATTCCAAAA
CTTATCATTGATCCACTGGGAGACTGGCTCATCAGTGCCTTTTTTTCAGAGGGAGAAGATCAAGTAAACATCCATGGATT
CATAAAAACTTTGGCTCATTTTGACCCACTGAAGATAGTGCAAAGAGCAAAGATAAGAATGGACCAGAGCCACTCAACAG
CCAAAGCAGCAAACTGTAGTTTGCTTTTTGACTATATGATTTGGATAAAGATGACCAGATCTCCTGTGATGAGCTGTTCC
AGGTGCTATGCATGGTGGTTGGAGTGAATATCTCAGATGAGCAACTGAGCAGTATCACAGACAGAACAATCCAGGAGGCT
TATCAGGATGGGTATGGCACCATATTTTTACCAGAGTTTGTTAAGGTTTTGGAGAAGGTGAACATAAAATGGAAAACAAA
CATCCTATTTTTAAAC

Alignment

ORF - retro_pvam_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.84 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRASTLLRDEELEEIKKETGF-SHSQITRLYSRFTSLDKGENG-TLSREDFQRIPELAINPLGDRIINAF
          S..S.LL..EEL.EIK.ETGF.S..QIT..YS.F...DK.E.G..LS.EDFQ.IP.L.I.PLGD..I.AF
Retrocopy SGVSMLL*REELKEIKEETGF<SYCQITHIYSQFANVDKVEKG<ALSQEDFQWIPKLIIDPLGDWLISAF

Parental  FPEGEDQVNFRGFMRTLAHFRPI-EDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVL
          F.EGEDQVN..GF..TLAHF.P..ED..KSKD.NGPEPLNS.S.KL.FAF.LYDLDKDD.IS.DEL.QVL
Retrocopy FSEGEDQVNIHGFIKTLAHFDPL<EDSAKSKDKNGPEPLNSQSSKL*FAF*LYDLDKDDQISCDELFQVL

Parental  RMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
          .M.VGVNISDEQL.SI.DRTIQEA.QDG...I...EFVKVLEKV....K..I.FL.
Retrocopy CMVVGVNISDEQLSSITDRTIQEAYQDGYGTIFLPEFVKVLEKVNIKWKTNILFLN

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_1207 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207 ,