RetrogeneDB ID: retro_pvam_400

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2932:186393..186806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E1
• Ensembl ID: ENSPVAG00000004322
• Aliases: None
• Description: solute carrier family 35, member E1 [Source:HGNC Symbol;Acc:20803]

Sequence

>retro_pvam_400
TCTCCGCGCTGCCATCGCACTGTACTTCCCATCATCAGTGGCATCCTGCTGGCCGCGGTCACACTTGTATTTTGACACGG
GAAGTGGGGAGCTGGTCAGAACTCTTGCTGGAACACTGTTTCTCACTTCAGAATAAATTCTCCAAAAAGGTATTGAGTGA
TTCAAAGCTCCGTGGCCTCCAGCCGCTGTACATCCAGGGCAGCCCCACCATCTTCTTTCAGATCTTTCTTGGGTTCTGGT
GGAACTTGTGGTTTTTCTTCTCGGCAAAAACTTGACCTGTGTTTCCCAGTGGCCCTGGAAGCTCCTGCTCTTCGCTGTCG
GGAGCTTCTGTAAGCTTTGCCCCAAATCTCATCATCTTCAGCTTTCTAAACCTGATCAGCTCTCCGAGCTACTCAGTCAC
CAATGTCACCAGG

Alignment

ORF - retro_pvam_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.35 %
• Parental protein coverage: 51.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STKVYLSLIPIISGV-LLATVTELSFDMWGL-ISALAATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCH
          S........PIISG..L.A.........WG...S.L....CFSLQN.FSKKVL.DS....L..L.I.G..
Retrocopy SPRCHRTVLPIISGILLAAVTLVF*HGKWGA<WSELLLEHCFSLQNKFSKKVLSDSKLRGLQPLYIQGSP

Parental  AVFFMI-PTWVLVDLSAFLVSSDLTYVYQWPWTLLLLAVSGFC-NFAQNVIAFSILNLISPLSYSVANAT
          ..FF.I...WVLV.L..FL....LT.V.QWPW.LLL.AV..FC..FA.N.I.FS.LNLIS..SYSV.N.T
Retrocopy TIFFQI<LSWVLVELVVFLLGKNLTCVSQWPWKLLLFAVGSFC>SFAPNLIIFSFLNLISSPSYSVTNVT

Parental  K
          .
Retrocopy R

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_400 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000004322	1 retrocopy	retro_pvam_400 ,