RetrogeneDB ID: retro_pvam_230

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2040:145535..145833(-)
• Located in intron of: ENSPVAG00000001900

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTA
• Ensembl ID: ENSPVAG00000012705
• Aliases: None
• Description: cystatin A (stefin A) [Source:HGNC Symbol;Acc:2481]

Sequence

>retro_pvam_230
ATGATGCCTGGAGGTTTAAATGAAGCCAAATCTGCCATTCTGGAAATCTAGGAGATTGCTAATGAGGTTAAACCACAGCT
TGAAGGAAAAATAAATGAGAATTATGATGAATTTGAAGCTGTAGAATACAAAACTCAAGTGGCTGCTAGAATAAATTACT
ATAAGTAATTAAGGTAGGAGTAGGTCATACTTATTATATTCACATGAAAATATTCAAAGCTCTTCCTCAACAAAATCAGT
CTTTGACACTTACTGGTTATCAGAATGACAAAAGCAAGACAATGAGCTGATAAGCTTT

Alignment

ORF - retro_pvam_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMPGGLTEAKPATPEIQEIANEVKPQLEEKTNETYEEFEVVEYKTQVVAGTNYYL-KVRVG--HNNYIHL
          MMPGGL.EAK.A..EI.EIANEVKPQLE.K.NE.Y.EFE.VEYKTQV.A..NYY.....VG..H..YIH.
Retrocopy MMPGGLNEAKSAILEI*EIANEVKPQLEGKINENYDEFEAVEYKTQVAARINYYK<VIKVGVGHTYYIHM

Parental  KIFKALPQQHQPLKLTGYQTDKSR-DDELTGF
          KIFKALPQQ.Q.L.LTGYQ.DKS..D.EL..F
Retrocopy KIFKALPQQNQSLTLTGYQNDKSK<DNELISF

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_230 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015604	1 retrocopy	retro_acar_24,
Mus musculus	ENSMUSG00000034362	1 retrocopy	retro_mmus_56,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Pteropus vampyrus	ENSPVAG00000012705	3 retrocopies	retro_pvam_230 , retro_pvam_601, retro_pvam_624,