RetrogeneDB ID: retro_pvam_824

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_12628:17664..18311(+)
• 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_824
TTGTACCAAATTGAATATGCTGTGGATGCGATTAGACATGCAGGCACCTGTTTGGGAATTTCAGCAAACGATAGTGTTTT
GCTTGAAGCAGAGGGATGCAACATCCGCAAGCTTCTTGATGAAGTCTTTTTTTCTGATATATTTATAAATTCAATGAAGA
CATGACTTACTGTGTGGCAGGCATAATTTCTGATACTAATGTTCTGACTAATGAACTCAGGCTCATTGTATTTATTACAG
TATCAGGAGCTTTTCCATGTGAGCAGCTGGTTACAGCACTGTGTGATATCAAACAAGCTTATACACAGTTTGAGGAAATA
TGTTCCTTTGGTGTTTCACTGTTGTACATTGACTGGGATAAGCACTATGACTTTCAGCTCTATGGAAGCAACCGTATGCG
GAAATTATGGGGGATGGAATGCCACATGCTTTGGAAATAACAGTGCTGCAGTTGTGTCAATATTGAAACAAGACTACAAA
TAAGGAGAAATGACTCTGAAGTCAGCACTTGCTTTAGCCGTCAAAGTCATCAATAAAACCATGGATGTTAGTAACTCTCT
GCTGAAAAAGTAGAATTTGCTGCACTAACAAGAGAAAGTGGAAAGATGGTTATCAGTTGATCAAAAAACATGGAGAAGAA
GAAGCTA

Alignment

ORF - retro_pvam_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.62 %
• Parental protein coverage: 83.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSE-KIYKLNEDMACSVAGITSDANVL
          LYQ.EYA..AI.HAGTCLGI.AND.VLL.AE..NI.KLLDEVFFS...IYK.NEDM...VAGI.SD.NVL
Retrocopy LYQIEYAVDAIRHAGTCLGISANDSVLLEAEGCNIRKLLDEVFFSD<YIYKFNEDMTYCVAGIISDTNVL

Parental  TNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSD-PSGN
          TNELRLI............PCEQLVTALCDIKQAYTQF.....FGVSLLYI.WDKHY.FQLY.S....GN
Retrocopy TNELRLIV---FITVSGAFPCEQLVTALCDIKQAYTQFEEICSFGVSLLYIDWDKHYDFQLYGSN>VCGN

Parental  YGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSK-LSAEKVEIATLTRESGKTV
          YGGW.ATC.GNNSAA.VS.LKQDYK.GEMTLKSALALA.KV.NKTMDVS..LSAEKVE.A.LTRESGK.V
Retrocopy YGGWNATCFGNNSAAVVSILKQDYK*GEMTLKSALALAVKVINKTMDVSN<LSAEKVEFAALTRESGKMV

Parental  IRVLKQKEVEQL
          I...K..E...L
Retrocopy IS*SKNMEKKKL

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_824 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,