RetrogeneDB ID: retro_pvam_121

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1513:59489..59862(-)
• Located in intron of: ENSPVAG00000014057

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000017748
• Aliases: None
• Description: None

Sequence

>retro_pvam_121
ATGCTGTCCCACCTGCTAAAGGAATACCAGGCCCAGCAGAATGAACGCAAGGAGCTACAGGAAAAAAGAAGGCAAGAGGC
TATCACTGCAGCGACCTGCCTGGCCAAAGCTTTGGTGAATCACCTCAATGTGGGTGTGGCCCAGGCCTACATGAACCAGA
GAAAGCTGGACCATGAAGTGAAGACCTTGCAGTTTCAGGCTGCCCAGTTTTCCAAGCAGATAGGCCAATGGATCGGAATA
GTGGAGAACTTCAACCAGGCACTAAGGAAATAGGGATGTGGAAAAATAGGCTCGGAGCATCGAGCTGGACATGCCACCAT
TGCCACTGCCCTGGAATACATCTACAAAGGACAGCTGTCAGTCAGCCCCATCC

Alignment

ORF - retro_pvam_121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
          MLS.LLKE.QA.QNERKELQEKRR.EAITAATCL..ALV.HLNVGVAQAYMNQRKLDHEVKTLQ.QAAQF
Retrocopy MLSHLLKEYQAQQNERKELQEKRRQEAITAATCLAKALVNHLNVGVAQAYMNQRKLDHEVKTLQFQAAQF

Parental  AKQTGQWIGMVENFNQAL-KEIG-DVENWARSIELDM-RTIATALEYVYKGQL-QSAQS
          .KQ.GQWIG.VENFNQAL.KEIG.DVE..ARSIELDM..TIATALEY.YKGQL.QSA.S
Retrocopy SKQIGQWIGIVENFNQAL<KEIG<DVEK*ARSIELDM<ATIATALEYIYKGQL>QSAPS

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_121 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Pteropus vampyrus	ENSPVAG00000017748	1 retrocopy	retro_pvam_121 ,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,