RetrogeneDB ID: retro_pvam_566

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3780:63232..64177(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000008661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSPVAG00000002945
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_pvam_566
ATTGGGATGGACTCCTGCGTCATACCCCTGAGACACGGAGGCTTGTCACTGGTGCAGACCACGGACTTCTTTTACCCCTT
GGTAGAAGATCCCTACATGATGGGGCGCATAGCTTGTGCCAACGTGCTAAGTGACCTCTATGCCATGGGCATTACTGAAT
GTGACAACATGTTGATGTTACTCGGCATCAGCCAGAATATGACTGAAGAGGAACGAGAAAAGATAACCCCAATGATGATC
AGAGGCTTCCGGGATGCTGCTGAGGAGGGAGGGACTGCAGTGACTGGTGGACAAACCGTGGTAAACCCTTGGATTATCGT
GGGTGGGGTTGCCACTGTGGTGTGTCAGCCAAATGAATTCATAATGCCTGACAGTGCAGTTGTTGGGGATGTGCTCGTGT
TAACCAAACCCTTAGGAACCCAAGTTGCTGTTAATGCCCACCAATGGCTAGATAATCCTGAAAGATGGAATAAGATAAAG
ATGGTGGTCTCCAGAGAAGAGGTAGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGCTACCCTAAACAGAACTGCTGC
TGGGTTAATGCACACATTTAATGCCCATGCAGCCACAGATATCACAGGCTTTGGCATTCTAGGACACTCCCAAAACCTTG
CAAAACAACAAAGAAATGAGGTGTCCTTCGTCATTCATAATCTGCCAATCATTGCCAAGATGGTTGCCATCAGCAAGGCC
AGTGGGCGGTTTGGGCTCCTTCAAGGAACCTCAGCAGAAACTTCTGGGGGATTACTGATTTGTTTGCCAAGGGAACAGGC
GGCTCGCTTTTGTTCTGAAATCAAATCTTCCAAGTATGGAGAGGGACACCAAGCATGGATCGTCGGCATTGTGGAAAAGG
GAAACCGGACTGCCCGGATCATTGACAAGCCTCGAGTTATTGAGGTCCTACCTCGTGGGGCCACT

Alignment

ORF - retro_pvam_566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDR
          IGMD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLLGIS..MT..
Retrocopy IGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLGISQNMTEE

Parental  ERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGT
          ER.K..P..I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTKPLGT
Retrocopy EREKITPMMIRGFRDAAEEGGTAVTGGQTVVNPWIIVGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGT

Parental  QVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHA
          QVAV..HQWLD.PE.WNKIK.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGILGH.
Retrocopy QVAVNAHQWLDNPERWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHS

Parental  QNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKY
          QNLAKQQRNEVSFVIHNLP..AKM.A.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EIKS.KY
Retrocopy QNLAKQQRNEVSFVIHNLPIIAKMVAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKY

Parental  GEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVAT
          GEGHQAWI.GIVEKGNRTARIIDKPR.IEV.P..AT
Retrocopy GEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGAT

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_566 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 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566 ,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,