RetrogeneDB ID: retro_pvam_753

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_10675:36987..37368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOXF1
• Ensembl ID: ENSPVAG00000009422
• Aliases: None
• Description: Rhox homeobox family, member 1 [Source:HGNC Symbol;Acc:29993]

Sequence

>retro_pvam_753
ATGGACTACATAGACCATGAAGTCCATGGGAACCACGAGGTCAACAGGAACCATGAGTGTGGCAGGAGTGACCAGGGGCC
TTGGCAGCAGCAGACTGAGATGACTCATGTGATGGCTGTGGCAGCTCCATAGCCCCAGAACAGGCAGCCATGAATCCAGC
GCAGTAAGTTCAGGCCTGCACAGCTGCAGGAGCTGGAAAGCACATTTGAACACACTCAATACCTGGATGTGCCCACAAGA
CAGGCACTTGTAAGCTGCATGGATGTGACTAAAACCAGAGTGCAGGTTTGATTTAAAAATAGGAGGACCAAGTATAGGAT
AAATGAGAGGGCATCGATATTTAGAAATGTACCACCCACTACCTGGAACCACCTTCTTATG

Alignment

ORF - retro_pvam_753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.34 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDMNHEGDIDHKGDQGNIDHGNHEGGGGDQETWQQQWFTVAVIALQNRQPRIQHNKFTPAQLQELESTF
          M....HE....H.....N...G....G...Q.T.......VA....QNRQP.IQ..KF.PAQLQELESTF
Retrocopy MDYIDHEVHGNHEVNR-NHECGRSDQGPWQQQTEMTHVMAVAAP*PQNRQP*IQRSKFRPAQLQELESTF

Parental  EHTRYLDAATRQELARHIDVTEAKVQVWLKNRKANYRKNERAPIFRNVLPATLNHLLL
          EHT.YLD..TRQ.L....DVT...VQV..KNR...YR.NERA.IFRNV.P.T.NHLL.
Retrocopy EHTQYLDVPTRQALVSCMDVTKTRVQV*FKNRRTKYRINERASIFRNVPPTTWNHLLM

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_753 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000009422	1 retrocopy	retro_pvam_753 ,
Ictidomys tridecemlineatus	ENSSTOG00000005297	1 retrocopy	retro_itri_735,
Tupaia belangeri	ENSTBEG00000002729	1 retrocopy	retro_tbel_3738,