RetrogeneDB ID: retro_pvam_490

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_345:148971..149493(-)
• Located in intron of: ENSPVAG00000000457

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSPVAG00000002807
• Aliases: None
• Description: stem-loop binding protein [Source:HGNC Symbol;Acc:10904]

Sequence

>retro_pvam_490
TATAAACGAAAACTTCACATAAGTGACTTCAAGAGAAAATCATCATCTGGAAGTTGTGGTTCAAAGAAGTGTGCATCTAC
AATATGAACAGAATTAGAAATAGATAGAAGTGTCCTGATGTAATGAAAAAAACAGATCTAACTATGGAGAAAACACCACT
GCTTATGATCAGTGTAGTAAAGAAGTTCCAAGGCATCTTTAACAACTAGACTTTCGTCCTAAGACATCTAACAACTTTAA
GAAGTACAGTCACAATCATAGGACAAGTAAATTAACCTGGGAGGTTGTTCTCATTCTTTGGATCTTCTAGCTAAAGAAGG
ATGTAATTTGCAAGAAATTCATCCCTTACAAGAAACCTTGGTGAAATGTAGATGCAGTCTAGAAAGTACTTCTGGATTCC
AGATAAGCTCTTGGGATGACTTAGATATGTACTCTGACATACTCACTGAAGTTAGACATGTGGACTGTCAAGGGGAGGAT
TAGTTTGATTTGAAAGACTTCTTAGCTATGAGCTTAGTCGAC

Alignment

ORF - retro_pvam_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.84 %
• Parental protein coverage: 67.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YKRKLLINDFGRERKSSSGSSDSKESASAVPADLETDEGVLMRRQKQI-SYGKNTLAYDRYIKAVPRHLR
          YKRKL.I.DF...RKSSSGS..SK..AS.....LE.D..VLM...KQI..YG.NT.AYD...K.VPRHL.
Retrocopy YKRKLHISDF--KRKSSSGSCGSKKCASTI*TELEIDRSVLM**KKQI>NYGENTTAYDQCSKEVPRHL*

Parental  QPGIHPKTPNKFKKYSRRSWDQQIKLWKVALHFW-DPPAEEGCDFQEIHPVDLGEMETEAA-ESSSGSQS
          Q....PKT.N.FKKYS..........W.V.L..W.D..A.EGC..QEIHP............ES.SG.Q.
Retrocopy QLDFRPKTSNNFKKYSHNHRTSKLT-WEVVLILW<DLLAKEGCNLQEIHPLQETLVKCRCSLESTSGFQI

Parental  SSQENLDVFSGTPTKVRHVDCQAEDEFDLEACLTEPLKD
          SS...LD..S...T.VRHVDCQ.ED.FDL...L...L.D
Retrocopy SSWDDLDMYSDILTEVRHVDCQGED*FDLKDFLAMSLVD

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_490 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490 , retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,