RetrogeneDB ID: retro_pvam_878

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_14495:1598..2027(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRIP2
• Ensembl ID: ENSPVAG00000014236
• Aliases: None
• Description: cysteine-rich protein 2 [Source:HGNC Symbol;Acc:2361]

Sequence

>retro_pvam_878
ATGGCCTCCAGGTGCCCCAAGTGCGACAAGACCGGATACTTCGCTGAGAAGGTGAGCTCCCCGGGCAAGGACTGGCACAA
GTTTTGCTTTAAGTGTGAGCGCCGCGGCACAACGGTGATGCCCGGGGGCCACGCCGAGCACAACCGGAAGCCATTTTGCC
ACAGCCCCGCTACGCCACACTGTTTGGACCCAAAGGGCTGAACATCGGAAGTGCTGGCTCCTACATCTACAAGAAGACTT
CTGAGGTGGGACCGCAGTCACTGGCCCCGTCGAGGTCCGCGTGGCCCGATTCGAGGAGCGCAAGGCGAGTGTCCCCCCAA
AGAGGCCCATCAAAGCCCTAGCATCACCACGTTCACCGAGGAACCCAAAATTTGTCCTCGCTGCAACAAAAGGATCTGCT
TTGCTGAGAAAGTGATGTCTCCCGGCCAA

Alignment

ORF - retro_pvam_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.15 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCGKTLTPGGHAEHDGKPFCHKPC-YATLFGPKGVNI
          MAS.CPKCDKT.YFAEKVSS.GKDWHKFC.KCER.G.T..PGGHAEH..KPFCH.P..YATLFGPKG.NI
Retrocopy MASRCPKCDKTGYFAEKVSSPGKDWHKFCFKCERRGTTVMPGGHAEHNRKPFCHSPA<YATLFGPKGLNI

Parental  GGAGSYIYEKPSAEGPQ-VTGPIEVPAARAEERKASGPPKGPSKA-SSVTTFTGEPNMCPRCNKRVYFAE
          G.AGSYIY.K.S..GPQ.VTGP.EV..AR.EERKAS.PPK.P.KA..S.TTFT.EP..CPRCNKR..FAE
Retrocopy GSAGSYIYKKTSEVGPQ<VTGPVEVRVARFEERKASVPPKRPIKA<PSITTFTEEPKICPRCNKRICFAE

Parental  KVTSLGK
          KV.S.G.
Retrocopy KVMSPGQ

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_878 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010504	1 retrocopy	retro_meug_481,
Pteropus vampyrus	ENSPVAG00000014236	1 retrocopy	retro_pvam_878 ,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000005041	2 retrocopies	retro_rnor_141, retro_rnor_2541,