RetrogeneDB ID: retro_pvam_53

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1155:143178..143617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSPVAG00000006344
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_pvam_53
ATGGCTTCTTCTGATGTCCAGGTGAAAGAACTGGAAAAGAGTGCCTCAGGACAGGCTTTTGAGCTGATTCTCAGCCCTAG
ATCAAAAGAATCTGTCCCAAATCCCCTCCTTCCCCTCTAAAGAAAGATCTTTCCCTGGAAGAATTCAGAAGAAATTAGGA
GCTTCAGAAGAAAGACGCAAATGCCATGAAGCTGAGGTCTTGAAACAGCTTGCTGAGAAACGAGAGCACAAGAAAAAAGT
GCTTCAGAAAGCAATCAAAGAAAACGACTTCAGTAAAATGGCAGACGAGAAACTGACCCACAAAATGGAAGCCAACAAAG
AGAACCGAGAGGCACAAATGGCTACCAAACTGGAGCATTTGCGAGAGAAGGACAAGCACATTGAAGAAGTATGGAAAAAC
AAAGAATCCAAAGATCCTGCTGATGCGACTGAAGCTGAC

Alignment

ORF - retro_pvam_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPEFPLSP-PKKKDLSLEE-IQKKLEAAEERRKSHEAEV
          MASSD.QVKELEK.ASGQAFELILSPRSKESVP..PL.P.P.KKDLSLEE.IQKKL.A.EERRK.HEAEV
Retrocopy MASSDVQVKELEKSASGQAFELILSPRSKESVPN-PLLP<PLKKDLSLEE<IQKKLGASEERRKCHEAEV

Parental  LKQLAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKXXXXXXXXXXXX
          LKQLAEKREH.K.VLQKAI.EN..FSKMA.EKLTHKMEANKENREAQMA.KLE.LREK............
Retrocopy LKQLAEKREHKKKVLQKAIKEND-FSKMADEKLTHKMEANKENREAQMATKLEHLREKDKHIEEVWKNKE

Parental  XXXXADETEAD
          ....AD.TEAD
Retrocopy SKDPADATEAD

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_53 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53 ,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,