RetrogeneDB ID: retro_pvam_842

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13363:19047..19369(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSPVAG00000003028
• Aliases: None
• Description: histidine triad nucleotide binding protein 2 [Source:HGNC Symbol;Acc:18344]

Sequence

>retro_pvam_842
TTCAAGAAGATTAATCGCAAGGAAATCCCAGCAAAAATAATTTTTGAGGATGACCAGTATCTTGCTTTTCATGACATTTT
TCCTCAAGCACCAACACATTTTCTGGTGATACCAAGAAGCAAAAATCCAAGATTTCTACAGCAGAAGATGATGATGAAAT
TCTTTTGGGACTTTTCATGATTGTTGGCAAGAAATGTGCTGCTGATATGGGCCTGAAGAAGGGTTATTGAATGGTGGTGA
ATGAGGCTCAGAGTGGGGACAGTCTGTCTATCATGTTCATCTCCATGTTCTTGGAGGTCAGCAGATGAACTGGCCTCTTG
GT

Alignment

ORF - retro_pvam_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.82 %
• Parental protein coverage: 66.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSRILDRSLPADILYEDQQCLVFRDVAPQAPVHFLVIPKKPIPR-ISQAEDEDQQLLGHLLLVAKNTAKA
          F..I.....PA.I..ED.Q.L.F.D..PQAP.HFLVIP....PR.IS.AED.D..LLG....V.K..A..
Retrocopy FKKINRKEIPAKIIFEDDQYLAFHDIFPQAPTHFLVIPRSKNPR<ISTAEDDDEILLGLFMIVGKKCAAD

Parental  EGLGDGYRLVIND-GKLAAQSVYHLHIHVLGGRQLQWPPG
          .GL..GY..V.N..G....QSVYH.H.HVLGG.Q..WP.G
Retrocopy MGLKKGY*MVVNE<GSEWGQSVYHVHLHVLGGQQMNWPLG

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_842 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201, retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842 ,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,