RetrogeneDB ID: retro_pvam_762

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_10963:28519..28905(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSPVAG00000004944
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_pvam_762
GAAACAAAGAAGTGTCGGTTGCTTCCTCTGGAGTGGATGGATGTGGAAAAGTTGGAGATTAGGGATCATGAGTGAGAAGA
AGAAACACTTACCCCCATGCCAAGCCCTTACTACATGGGACTTACAAACTCTTGTTAAATTATACTTCAGACAATGTCCC
AAAAGCAGATGAGCCCCTGATCAAGAATGTGTGGGACACCAGCATAGCCAAACTTTTGGTGTCTTATGACAGCTTTGTGA
GGCAGCAGGAGACAAATGTCAAACTGGATAATTCGACCATGACGGAGATTACTACCAGTGAAGGTTTCCTCACACAAGCA
CTCAATCACATATACAAACTCCACACAAATTTTCAAACTCCTGAAAGTGCCCAGACTAAGGACTTC

Alignment

ORF - retro_pvam_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 71.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRQKCRLLPPEWMDVEKLEKIRDHERKEETFTLMPSPYYMELT-KLLLNHASDNIPKADEIRTLIKDVWD
          ...KCRLLP.EWMDVEKLE.IRDHE..EET.T.MPSPYYM.LT.KLLLN..SDN.PKADE...LIK.VWD
Retrocopy ETKKCRLLPLEWMDVEKLE-IRDHE*EEETLTPMPSPYYMGLT<KLLLNYTSDNVPKADE--PLIKNVWD

Parental  TRIAKLRVSADRFVRQQEVHAELDNLTLMEINTSGAFLTQALNHMYKLRTNLQPSDSAQSQDF
          T.IAKL.VS.D.FVRQQE....LDN.T..EI.TS..FLTQALNH.YKL.TN.Q...SAQ..DF
Retrocopy TSIAKLLVSYDSFVRQQETNVKLDNSTMTEITTSEGFLTQALNHIYKLHTNFQTPESAQTKDF

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_762 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762 ,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,