RetrogeneDB ID: retro_pvam_115

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1451:36393..37085(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_pvam_115
GGGGTCACAGAATGTGACAATATGCTGAAGTTCCAAATCAGGAATAATATGACCAACAGAGAAAGGGATAAAGTGATGCT
ACTAATTACACAGGGTTTTAAAGATGCAGCAGAAGAGGCAGGAACATCTGTAGTGGGTGGCCAAACAGTGTTAAACCCCT
GTATTGTTTTGGGAGGAATGGCTACAACTGTCTGCCAGCCTAATGAATTCATTGTGCCAGACAAAGCAATGCCTGAGGAT
GTGCTCGTGCTCACAAAGCCCCTAGAGATGCAGGTGGCCATGGCCATGCACCAATGTCTGGATATTCCCGAAAAATGGAA
TGAAATTAAACTAGTGGTGACCCAAGAAGATGTGGAGTTGGCAGAGCAGGAGGTGATGATGAACATGGCAAGGTTCAACA
GAACAGATGCAGGACTCACATACACATCCAAGCCCACACTGCCACCAACATCCCGGGGCTTTGGAATTCTGGGCCACCAC
AGAACCTAGCCAAACAACGGAGGAAGAAGGGGTCCTTAGTGATTCACAACCTCCCTGTCCTGGCTGAGATGGCTGTTGTG
AGCAAGGCCTGTGGAAACATGTTTGGCCTCATGCATGGGGACTGTCCTGAGACATCAAGAGACTTTCTAATCTGTTTACC
CTGTTAGCAAGCCACTTAGCTCTGAGCAGAGATAAAGTCCCCTAAATATGGT

Alignment

ORF - retro_pvam_115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 59.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GVTECDNMLMLLGISNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNE
          GVTECDNML....I.N.MT.RERDKVM.LI.QGFKDAAEEAGTSV.GGQTVLNP.IVLGG.ATTVCQPNE
Retrocopy GVTECDNMLKFQ-IRNNMTNRERDKVMLLITQGFKDAAEEAGTSVVGGQTVLNPCIVLGGMATTVCQPNE

Parental  FIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGL
          FI.PD.A.P.DVLVLTKPL..QVA.A.HQ.LDIPEKWN.IKLVVTQEDVELA.QE.MMNMAR.NRT.AGL
Retrocopy FIVPDKAMPEDVLVLTKPLEMQVAMAMHQCLDIPEKWNEIKLVVTQEDVELAEQEVMMNMARFNRTDAGL

Parental  MHT-FNAHAATDI-TGFGILGH-AQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETS
          ..T...AH.AT.I..GFGILGH..QNLAKQ.R...S.VIHNLPVLA.MA.VSKACGNMFGLMHG.CPETS
Retrocopy TYT<IQAHTATNI>RGFGILGH<PQNLAKQRRKKGSLVIHNLPVLAEMAVVSKACGNMFGLMHGDCPETS

Parental  GGLLICLPREQAARFCAEIKSPKYG
          ...LICLP..QA....AEIKSPKYG
Retrocopy RDFLICLPC*QAT*L*AEIKSPKYG

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_115 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,