RetrogeneDB ID: retro_pvam_261

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2232:264085..264647(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LITAF
• Ensembl ID: ENSPVAG00000009213
• Aliases: None
• Description: lipopolysaccharide-induced TNF factor [Source:HGNC Symbol;Acc:16841]

Sequence

>retro_pvam_261
GCTCCAGGACCCGACCAGTCAGCGGTTGGGCCTTCGTCACTGCCCACAGCGCCCGCGTCCTATGAAGAGACAGTAGCGGT
TAACAGTTACTTCCCCACGCCTCCGCACCCATGCCTGGGCCAGCGACAGGGCTCACGGCAGGCCAGATGGAAAGGGCATG
AACCCACCTGCGTACTACATCTAGCCAGTGCCGGTCTCCAACTCCAATGCAATTGCTGTGCAGACGGTCAACATGCAGCA
GCCAGTCTCCTTTATCGACCGCCCAGCGCAGATGTGTTGTCCTTCCTGTAACAAGATGATTGTGACTCAGCTGTCCCATA
AAGCCGGTGTTCTCACCTGGCTCTCCTGTGGGAGCCTGTGCCTGCTCGGGTGCGTAGCAGGCTGCTGTTTCATCCCTTTC
TATGTGGACGCTCTGCGGGACGTGGACCATTACTGTCCCAACTGCAAAGCTCTCCTGGGCACCTACAAGCGTTTGTAGGA
CTCGGCCAAACCTGGAGGGTTCCGTGTTGTGGCAAGAAGTCCTTTTCGACTCTCACCCAGCCTCACCCCTGGTGGAGATC
TC

Alignment

ORF - retro_pvam_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 82.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  APGPYQAAAGPSSVPTAPPSYEETVAVNRYYTTPP-APMPGPATGLMTG-PDGKGMNPPAYYTQPGPVPN
          APGP.Q.A.GPSS.PTAP.SYEETVAVN.Y..TPP.APMPGPATGL..G.PDGKGMNPPAYY..P.PV.N
Retrocopy APGPDQSAVGPSSLPTAPASYEETVAVNSYFPTPP<APMPGPATGLTAG<PDGKGMNPPAYYI*PVPVSN

Parental  ANAIAVQTVYVQQPVSFFDRPVQMCCPSCNKMIVTQLSYNAGALTWLSCGSLCLLG-VRSGLLFHPFLCG
          .NAIAVQTV..QQPVSF.DRP.QMCCPSCNKMIVTQLS..AG.LTWLSCGSLCLLG.VRS.LLFHPFLCG
Retrocopy SNAIAVQTVNMQQPVSFIDRPAQMCCPSCNKMIVTQLSHKAGVLTWLSCGSLCLLG<VRSRLLFHPFLCG

Parental  RSAGRGPLLSQLQSSPGHLQAFVGLGQTWREPC-VAGSPFRLSPSPAPGGDI
          RSAGRGPLLSQLQSSPGHLQAFVGLGQTWR.PC.VA.SPFRLSPS..PGGD.
Retrocopy RSAGRGPLLSQLQSSPGHLQAFVGLGQTWRVPC>VARSPFRLSPSLTPGGDL

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_261 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261 ,
Pteropus vampyrus	ENSPVAG00000016131	1 retrocopy	retro_pvam_342,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,