RetrogeneDB ID: retro_pvam_601

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3994:138389..138608(-)
• Located in intron of: ENSPVAG00000005018

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_601
ATGATGCCTGGAGGTTTAATTGAAGCCAAACCTGCCACTCTAGAAATCAAGGAGATTGCTAATGAAGTTAAATCATAGCT
TGAAGGAAAAACAAATGAGACTTAGGAAGAATTTGAAGCTGTAGAATACAAAACTCAAGTGGTTGCTGGAAAAAATTACT
ACATTAAGGTACGAGTAGGTCATAATATTTATATCTACCCGAAAACATTCAAAGCTCTT

Alignment

ORF - retro_pvam_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 74.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMPGGLTEAKPATPEIQEIANEVKPQLEEKTNETYEEFEVVEYKTQVVAGTNYYLKVRVGHNNYIHLKIF
          MMPGGL.EAKPAT.EI.EIANEVK..LE.KTNET.EEFE.VEYKTQVVAG.NYY.KVRVGHN.YI..K.F
Retrocopy MMPGGLIEAKPATLEIKEIANEVKS*LEGKTNET*EEFEAVEYKTQVVAGKNYYIKVRVGHNIYIYPKTF

Parental  KAL
          KAL
Retrocopy KAL

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_601 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,