RetrogeneDB ID: retro_pvam_618

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_4066:304182..304622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSPVAG00000006048
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_pvam_618
TCCTATATTGCTATTCGAGTGACTGACAAGTTGGCCCCTATTCATGATTGTATTTTCTGCTGCCACTCAGGCTCCGCAGC
TGATACCTAGGCGGTGGCTGATGCTGTTACCTACCAGCTTGGTTTCCACAGCATTGGACTGAATGAGCCTCCACTGGTAC
ACACAGCAGCCAGCCTCTTTAAGGAGATGTGTTACCGATACCAGGAAAGACCTGATGACAGGAATCTTCACTGTGGGTTG
GGACCCCCAAGAAAGAGGGCAGGTGTACTCAGTGCCCATGGCGGGTATGATGGTAAGGCAGTCCTTTGTCACTGGAGGCT
CCAGGAGCTCCTATATCTTATGGCTATGTCAATGCTACCTACTGGGAAGGCATAACTAAGGAAGAGTGTCTGCGGTTCAC
TGCCGATGCTCTTGCTTTGGCCATGGAGCTGGACGGCTCC

Alignment

ORF - retro_pvam_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRY-RE
          SYIA.RVTDKL.PIHD.IFCC.SGSAADT.AVADAVTYQLGFHSI.LNEPPLVHTAASLFKEMCYRY.R.
Retrocopy SYIAIRVTDKLAPIHDCIFCCHSGSAADT*AVADAVTYQLGFHSIGLNEPPLVHTAASLFKEMCYRY>RK

Parental  DLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYI-YGYVDATYREGMTKEECLQFTANALA
          DLM.GI...GWDPQE.GQVYSVPM.GMMVRQSF..GGS.SSYI.YGYV.ATY.EG.TKEECL.FTA.ALA
Retrocopy DLMTGIFTVGWDPQERGQVYSVPMAGMMVRQSFVTGGSRSSYI>YGYVNATYWEGITKEECLRFTADALA

Parental  LAMERDGS
          LAME.DGS
Retrocopy LAMELDGS

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_618 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618 ,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807,