RetrogeneDB ID: retro_pvam_1185

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3867:97217..97793(-)
• 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_1185
ATACCAAACATCATATTTGTTGGTGGAATTGATGTTAGGATAGATAACACTGAAATTAGAAGTTTCTTTGCTAGATATGG
TTCAGTAAAAGAAGTGAAGATAATCATGGATTGAACTGATTTGTCTAAAGGTTATGGATTTGTTTCCTTTTATAATAATG
CAGATGTGCAGAAGACAGTAGAATCACAGATAAATTTCCATGGTAGAAAGCTGAAACTGGGCCCTACAATCAGGAAACAA
AATTTACGTCCTTATCATGTACAGCCATGTCCTTTGGTTTTTAATCCTCCTCATTCATCATAGTTTGAGAGTGTCTGGAG
TAATCTAAACACTAAAATTTTATGCAGCATTCAACAATGTGAATCCTATAACTCAGTATATTCAGATATATCTTCCTTAC
GGAAGTTCATCACTTCAGGTCATCACTGGATATCAGTTGCCCGTATATCAGATGCCACCACAGTGGCCTGCTGGGAACAA
AGGAGTTATGTTATACCTCCAGCTTATACAGTTGTTATCTACCACTGTAATGAAGTTGATTCAGGAGCTGAAGTTTTGTC
TAGTGAATGCTCCATC

Alignment

ORF - retro_pvam_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPNTVFVGGIDIRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQINFHGKK
          .PN..FVGGID.R.D.TEIRSFFARYGSVKEVKII.D.T..SKGYGFVSFYN..DVQK.VESQINFHG.K
Retrocopy IPNIIFVGGIDVRIDNTEIRSFFARYGSVKEVKIIMD*TDLSKGYGFVSFYNNADVQKTVESQINFHGRK

Parental  LKLGPAIRKQNLCAYHVQPRPLVFNPPPPPQFQSVWSNPNTE-TYMQPPTM-MNPITQYVQTYPPYPSSP
          LKLGP.IRKQNL..YHVQP.PLVFNPP....F.SVWSN.NT....MQ..TM..NPITQY.Q.Y.PY.SS.
Retrocopy LKLGPTIRKQNLRPYHVQPCPLVFNPPHSS*FESVWSNLNTK<NFMQHSTM<VNPITQYIQIYLPYGSSS

Parental  VQVITGYQLPVYNYQMPPQW-AG-EQRSYVIPPAYTTVNYHCNEVDSGAEVLQSECSV
          .QVITGYQLPV..YQMPPQW.AG.EQRSYVIPPAYT.V.YHCNEVDSGAEVL.SECS.
Retrocopy LQVITGYQLPV--YQMPPQWPAG<EQRSYVIPPAYTVVIYHCNEVDSGAEVLSSECSI

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_1185 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.

---

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,