RetrogeneDB ID: retro_pvam_1451

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_89839:2..403(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSPVAG00000001773
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_pvam_1451
ATGTCAGATGACAGTTTGAAGGCAAACACCAGCTCCTCCTCATCTTCGTCTTCCAATCAGCAAACCAAGAAATAAACACC
CTCAAGAAAAAGGAGCATAAAGTCAGCATGAACAAAAACTCCAAACTCCTCTCCATCAACGCCAAGACGATTTGGAAGGA
ACTGGCAGGTATCACTTTAGACCCTTCACCTAGCTCCGGTGCTGGTCCCAAAGGTGATAACATCTGTGAATGGAGATCAA
CCATTCTAGGGCCACCAGGATCTGTTTGCAAGGGTGATATGACTCTCTCTGATATCTCTTTTACACCAGAATATCCCTTC
AAGCCTCCAAAGGTTACATTTTGGACAAGAATCTATCCCTGTAATATTAACAGTAAAGGAATTATTTGCTTGGACATACT
G

Alignment

ORF - retro_pvam_1451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 83.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDDDSKTSTSSSSSSSSNQQTEK-ETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSA
          MSDD..K..TSSSSS.SS..Q..K.E.NT.KKKE.KVSM.KNSKLLS..AK.I.KELA.ITLDP.P...A
Retrocopy MSDDSLKANTSSSSS-SSSNQQTK<EINTLKKKEHKVSMNKNSKLLSINAKTIWKELAGITLDPSPSSGA

Parental  GPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDIL
          GPKGDNI.EWRSTILGPPGSV..G.....DI.FTPEYPFKPPKVTF.TRIY.CNINS.G.ICLDIL
Retrocopy GPKGDNICEWRSTILGPPGSVCKGDMTLSDISFTPEYPFKPPKVTFWTRIYPCNINSKGIICLDIL

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_1451 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451 ,
Pteropus vampyrus	ENSPVAG00000007394	2 retrocopies	retro_pvam_1139, retro_pvam_363,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,