RetrogeneDB ID: retro_pvam_1349

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_6592:50500..51099(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFD1L
• Ensembl ID: ENSPVAG00000006417
• Aliases: None
• Description: ubiquitin fusion degradation 1 like (yeast) [Source:HGNC Symbol;Acc:12520]

Sequence

>retro_pvam_1349
GATGAGGGTATCTGCTACCTCCCATACTGGATGATGCAGAATTTGCTGTTAGAAGAAGGGGGACTGGTTCAGGTGGAGAG
TGTCAATCTGCAAGTGGCCACATACTCCAAATTTCAGCTTCAGAGCCCTGACTTCCTGGATATCACCAACCCCAAAGCAG
TATAAGAAAATGCACTGAGAAACTTTGCCTGAACACCGGGGATGTGATTGCCATCAACTACAATGAGATCTATGAACTGC
GGGTGATGGAGACCAAGCCTGACAAAGCTGTGTCCATCACTGAGTGCGACATGAATGTGGACTTTGATGCTCCACTGGGC
TACAAAGAACCTGAAAGACAAGTCCAGCATGAGGAGTCAACTGAAGGCAAAACTGACCACAGAGGCTATGCTGGAGAGCT
GGGCTTCCATGCCTTCTCCGGCTCTGGGAACAGACTGGATGGGAAGAAGAAAGATGTAGAGCTGAGTGCCTTCCCAATCA
AGCCTGGAGACATTAAAAGAGGAATTCCCAATTACGAATTTAAACTTGGTAAGATCACTTTCATCAGAAATTCACGTCCA
CTGGTCAAAAAGGTTGAAGAGGATGAAGCTGGAGGCAGA

Alignment

ORF - retro_pvam_1349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRSLYGLRVWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITN-PKAVLENALRNFACLTTGD
          D.....L..WMMQNLLLEEGGLVQVESVNLQVATYSKFQ.QSPDFLDITN.P............CL.TGD
Retrocopy DEGICYLPYWMMQNLLLEEGGLVQVESVNLQVATYSKFQLQSPDFLDITN<PQSSIRKCTEKL-CLNTGD

Parental  VIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEESTEGETDHSGYAGELGFR
          VIAINYNE.IYELRVMETKPDKAVSI.ECDMNVDFDAPLGYKEPERQVQHEESTEG.TDH.GYAGELGF.
Retrocopy VIAINYNE-IYELRVMETKPDKAVSITECDMNVDFDAPLGYKEPERQVQHEESTEGKTDHRGYAGELGFH

Parental  XXXXXXNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGR
          ......NRLDGKKK.VE.S..PIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGR
Retrocopy AFSGSGNRLDGKKKDVELSAFPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGR

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_1349 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004294	1 retrocopy	retro_fcat_604,
Homo sapiens	ENSG00000070010	1 retrocopy	retro_hsap_1929,
Gorilla gorilla	ENSGGOG00000004104	1 retrocopy	retro_ggor_175,
Myotis lucifugus	ENSMLUG00000002466	1 retrocopy	retro_mluc_1244,
Macaca mulatta	ENSMMUG00000031106	1 retrocopy	retro_mmul_1347,
Pongo abelii	ENSPPYG00000011580	1 retrocopy	retro_pabe_1593,
Pteropus vampyrus	ENSPVAG00000006417	1 retrocopy	retro_pvam_1349 ,