RetrogeneDB ID: retro_pvam_1209

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_42418:3404..4172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5A
• Ensembl ID: ENSPVAG00000010468
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', alpha [Source:HGNC Symbol;Acc:9309]

Sequence

>retro_pvam_1209
GTAGACGGATTTTCTCGGAAGTCTGTCAGAAAAGCCAGACAGAAGTCGCAAAGTTCCTCACAGTTTAGATCTTGAGGCGA
GCCTATTGAGTTAACACCTCTGCCACTGCTGAAAGACATTATGCCCTCAGAGCTCCCTGGACTTTTCTCAAAGAAACATC
AGCAGTGCTGTGTCATTTTCAACTTCACCAACACGCGATCCGATCTTAAAATGAAAGAATACAAGCGCTCCACTCTTAAT
GAACTGGTAGACTACATTGCAATAAGCAGAAGCTGTTTGGCAGAGCAGACTTACCCTGAAGGAGTTAGAATGGTATCTTG
CAATATATTCAGAACTCTCCCCCACAGTGAGAGCAATGGATTGAATCCAGAAGAAGATGAACCTGAACCTACCTTTGGGG
CGTCATGCCCATACTTACAGCTTGTATATGCATTTTTCATACTATTTTTGGAAAGCCAAAAATCCCAACCTAGCATTGCC
AAAATAATACGTAGATCAGAAATTTGTATTACAGTTTTTGGAGCTACTTGACAGCAAAGACCCCTGGGAGTGGGACTACT
TAAAAACAGTTTTACACAGAATTTATGACAAGTTTTTTGGTCTTAGAGCGTTCATCTGAAAACAGATTAACACGATTTTT
CTAAGGCTGTTTATGAACAGAATACTTCAATGGTGTAGCCAGACGGCTGCTGGGAATATTAAAAAGTATTACCGATGGTT
TGTTCTATCTCTTACGCAGAACACAAACAGTTTCTGTGTAAGATTATT

Alignment

ORF - retro_pvam_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 52.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VDGFTRKSVRKAQRQKRSQGSSQFRSQGSQAELHPLPQLKDATSNEQQELFCQKLQQCCILFDFMDSVSD
          VDGF.RKSVRKA.....SQ.SSQFRS.G...EL.PLP.LKD....E...LF..K.QQCC..F.F....SD
Retrocopy VDGFSRKSVRKARQ--KSQSSSQFRS*GEPIELTPLPLLKDIMPSELPGLFSKKHQQCCVIFNFTNTRSD

Parental  LKSKEIKRATLNELVEYVSTNRGVIVESAYSDIVKMISANIFRTLPPSDNPDFDPEED--EPTLEASWPH
          LK.KE.KR.TLNELV.Y....R....E..Y...V.M.S.NIFRTLP.S......PEED..EPT..AS.P.
Retrocopy LKMKEYKRSTLNELVDYIAISRSCLAEQTYPEGVRMVSCNIFRTLPHSESNGLNPEEDEPEPTFGASCPY

Parental  IQLVYEFFLRFLESPDFQPSIAKR-YIDQKFVQQLLELFDSEDPRERDFLKTVLHRIYGK-LGLRAFIRK
          .QLVY.FF..FLES...QPSIAK..Y.DQKFV.Q.LEL.DS.DP.E.D.LKTVLHRIY.K..GLRAFI.K
Retrocopy LQLVYAFFILFLESQKSQPSIAKI>YVDQKFVLQFLELLDSKDPWEWDYLKTVLHRIYDKFFGLRAFI*K

Parental  QINNIFLRF-IYE-TEHFNGVA-ELLEILGSIING-FALPLK-AEHKQFLMKVL
          QIN.IFLR...YE.TE.FNGVA..LL.IL.SI..G.F.L.L..AEHKQFL.K..
Retrocopy QINTIFLRL<VYE<TEYFNGVARRLLGILKSITDG<FVLSLT<AEHKQFLCKII

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_1209 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
Myotis lucifugus	ENSMLUG00000009549	1 retrocopy	retro_mluc_1768,
Mus musculus	ENSMUSG00000026626	5 retrocopies	retro_mmus_2410, retro_mmus_2415, retro_mmus_2417, retro_mmus_2421, retro_mmus_3390,
Pteropus vampyrus	ENSPVAG00000010468	1 retrocopy	retro_pvam_1209 ,
Rattus norvegicus	ENSRNOG00000000068	1 retrocopy	retro_rnor_2107,
Tarsius syrichta	ENSTSYG00000013786	1 retrocopy	retro_tsyr_1135,
Vicugna pacos	ENSVPAG00000011662	1 retrocopy	retro_vpac_63,