RetrogeneDB ID: retro_pvam_1229

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_45877:555..1277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA4
• Ensembl ID: ENSPVAG00000009182
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 4 [Source:HGNC Symbol;Acc:9533]

Sequence

>retro_pvam_1229
TACCAAGTTGAATGACTTGGAAGCAATGCAGGCACCTCTTTGGAAATTTTAGCAGATGATGGTGTTTTGCTTGCAGTAGA
AAGATGAAAAATCCACAAGCTTCTTGATGATGTCTTTTTTTCTGAAGAGATTTATAAACTCAATGAGGACATGGCTTGCA
GTGTGGCAGGCATAACCTGTGATGCTAATGTTCTGACTAATGAATTGAGGCTTATTGCTCAAAGGTACTTATTACAGTAT
CAGGAGCCAATTCTTTATGAGTGGTTGGTTATGACACTTTTGTGTGATAGCAAACAAGCTTATGCACAGTTTGGAGGAAA
ACCTCACTTTGATGTTTCACTGTTGTACATTGGCTAGGATAAGCACTAGGGCTTTCAGCTCTATCAGAGCTATGCTAGCG
GAAATAATGGGGGATGGAAAGCCACATGCATTGGAAATAATAGCGCTGCAGCTGTGTCAACATTAAAACAAGACTAAAAA
GAAGAAACATGACTCGGAAGTCAGCAGTTGCTTTAGCTATCAAAAGTTTTCAATAAGACCACGAATATTAGCAAACTCTG
TGCCGAAAAAGTGAAAATTGCCACACTAACAGGAGAGAGTGGAAAGATGATCATCAGAGTTCTCAAAAAAGGAAGTGGAA
TCGTTGATCAAAAAAACATGAGGAAGAAGAAGCTAAAGCTGAGCATGAGAAGGAAGAAAAAGAACAAAAAGGAAAGGATA
AA

Alignment

ORF - retro_pvam_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 91.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YAMEAIG-HAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELR
          Y..E..G..AGT.L.ILA.DGVLLA.ER..IHKLLD.VFFSE.IYKLNEDMACSVAGIT.DANVLTNELR
Retrocopy YQVE*LGSNAGTSLEILADDGVLLAVER*KIHKLLDDVFFSEEIYKLNEDMACSVAGITCDANVLTNELR

Parental  LIAQRYLLQYQEPIPCEQLV-TALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWK
          LIAQRYLLQYQEPI..E.LV.T.LCD.KQAY.QFGGK..F.VSLLYIG.DKH.GFQLYQS..SGN.GGWK
Retrocopy LIAQRYLLQYQEPILYEWLVMTLLCDSKQAYAQFGGKPHFDVSLLYIG*DKH*GFQLYQSYASGNNGGWK

Parental  ATCIGNNSAAAVSMLKQDYKE-GEMTLKSALALAI-KVLNKTMDVSKLSAEKVEIATLTRESGKTVIRVL
          ATCIGNNSAAAVS.LKQD.KE...MT.KSA.ALAI.KV.NKT...SKL.AEKV.IATLT.ESGK..IRVL
Retrocopy ATCIGNNSAAAVSTLKQD*KE<RNMTRKSAVALAI>KVFNKTTNISKLCAEKVKIATLTGESGKMIIRVL

Parental  K-QKEVEQLIQKHEEEEAKAEREKKEKEQKEKDK
          K..........KHEEEEAKAE.EK.EKEQK.KDK
Retrocopy K<KRKWNR*SKKHEEEEAKAEHEKEEKEQKGKDK

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_1229 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Pteropus vampyrus	ENSPVAG00000009182	2 retrocopies	retro_pvam_1229 , retro_pvam_824,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,