RetrogeneDB ID: retro_pvam_674

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_65:29925..30486(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZL
• Ensembl ID: ENSPVAG00000007836
• Aliases: None
• Description: deleted in azoospermia-like [Source:HGNC Symbol;Acc:2685]

Sequence

>retro_pvam_674
ATTTCCAGAGAGGCCAGCACCCAGTACTCGTCAGCTACAACTAGCCAAGGCTATGTTTTACTTGAAGGCAAAATCATGCC
AAACATAATTTTTGTTGGTAGAACTGATGTTAGGATGGATGAAACCAAAATTAAAAGTTTCTTTGCTAGATATGGTTCAG
TAAAAGAAATGAAGAGAATCACCGATTGAACTGGTATGCCCAAAGGCTATGGATTTGTTTCTGTTTATAATGACATGGAT
GTTCAGAAGATAGTAGAATCACAGAAAAATTTCCATGGTAAAAAGTTGAAACTGGGCCCTGCAGTCGGGAAACAAAATTT
ATGTACTTATCACGTGCAGCCACATCCTGTGGTTTTTAATCCTTTTCATCCACCACAGTTACGGAGTGTCTGGAGTAATC
CAAACACTGAAACTTATATACAGCCTTCAAACATGATGATCCTATAACTCAGTATGTTCAGGCATTTTCTCCTTATCCAA
GTTCACCAATCAGGTCATCACTGGATATCAGGTGCCTGTATATAATTATCAGATGTCATACAGTGGTCTGCTGATCAAAA
G

Alignment

ORF - retro_pvam_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.96 %
• Parental protein coverage: 63.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISREASTQSSSATTSQGYVLPEGKIMPNTVFVGGIDIRMDETEIRSFFARYGSVKEVKIITDRTGVSKGY
          ISREASTQ.SSATTSQGYVL.EGKIMPN..FVG..D.RMDET.I.SFFARYGSVKE.K.ITD.TG..KGY
Retrocopy ISREASTQYSSATTSQGYVLLEGKIMPNIIFVGRTDVRMDETKIKSFFARYGSVKEMKRITD*TGMPKGY

Parental  GFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQNLCAYHVQPRPLVFNPPPPPQFQSVWSNPNTETYM
          GFVS.YND.DVQKIVESQ.NFHGKKLKLGPA..KQNLC.YHVQP.P.VFNP..PPQ..SVWSNPNTETY.
Retrocopy GFVSVYNDMDVQKIVESQKNFHGKKLKLGPAVGKQNLCTYHVQPHPVVFNPFHPPQLRSVWSNPNTETYI

Parental  QPPTMM-NPITQYVQTYPPYPSSPV-QVITGYQLPVYNYQMP-PQWAGEQR
          QP..MM..PITQYVQ...PYPSSP..QVITGYQ.PVYNYQM...QW...Q.
Retrocopy QPSNMM<DPITQYVQAFSPYPSSPI<QVITGYQVPVYNYQMS<IQWSADQK

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_674 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007628	1 retrocopy	retro_cpor_637,
Otolemur garnettii	ENSOGAG00000006983	1 retrocopy	retro_ogar_1070,
Pteropus vampyrus	ENSPVAG00000007836	2 retrocopies	retro_pvam_1185, retro_pvam_674 ,