RetrogeneDB ID: retro_pvam_1028

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2340:49763..50401(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN3
• Ensembl ID: ENSPVAG00000006191
• Aliases: None
• Description: bridging integrator 3 [Source:HGNC Symbol;Acc:1054]

Sequence

>retro_pvam_1028
GTGGAGAGAGACTTTGAAAGGGAGTATGAAAAACTCCAGCAACTGAAAGAACAAACCAAGAGGATGCAGAAGGACATGAA
GGAGAGCACCAATTTTGATCTGGCCATGTCCAAATCTGCTCTGAAAATATCCTTAGATTTACTCTCTAATCCTCTCTACA
AGCAAGGCCAGAACTTTCTGAACATAGTGACAGCTCTGGACATGGACATGAAGTAGATGGATGCCTTCAACCAGGAAAAG
GTGAACCAGATCCAGAAGACATTGATTGAACCCTTAAAAAAGTTTGGCAATGGCTTCCCAAGCATTAAATGGCAGTGAAA
CAGCAGAAGCATGTTTTATAGGATTATAGGAGATTGAAGGCCAAGATGGAGAAGTATAAGGAAAAGGAAAAAACAGAACC
AGTGCTGGCTAAACTCTACCAGGCCTAAGAAGAGCTTTAGCCTATGTGGGATGACTTGAAAGCCAAGATCAAGCAGCTCC
TGGATGAGATGCTGCAGTTCTACCACAGCCAACTTGACTACATCCAACACAGCTTTGAGTCCCTGATAAGAGCACAGATG
GTACACTACTCTGAAATGCTTAAGATCTTTGGAGATTTGACCCAGCAACTTGACCAGCCTGGCCACCCAGACAAGCAG

Alignment

ORF - retro_pvam_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 91.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VERDFEREYGKLQQLEEQTRKLQKDMKKSTDADLAMSKSAVKISLDLLSNPLCEQDQDFLNMVTALDTAM
          VERDFEREY.KLQQL.EQT...QKDMK.ST..DLAMSKSA.KISLDLLSNPL..Q.Q.FLN.VTALD..M
Retrocopy VERDFEREYEKLQQLKEQTKRMQKDMKESTNFDLAMSKSALKISLDLLSNPLYKQGQNFLNIVTALDMDM

Parental  KRMDAFNQEKVNQIQKTVIEPLKKFGSVFPSLN-MAVKRREQALQDYRRLQAKVEKYEEKEKTGPVLAKL
          K.MDAFNQEKVNQIQKT.IEPLKKFG..FPS...MAVK.....L.DYRRL.AK.EKY.EKEKT.PVLAKL
Retrocopy K*MDAFNQEKVNQIQKTLIEPLKKFGNGFPSIK<MAVKQQKHVL*DYRRLKAKMEKYKEKEKTEPVLAKL

Parental  HQAREELRPVRNDFEAKNKQLLDEMPRFYNSRLDYFQPSFESLIRAQVVYYSEMHKIFGDLTQQLDQPGH
          .QA.EEL.P...D..AK.KQLLDEM..FY.S.LDY.Q.SFESLIRAQ.V.YSEM.KIFGDLTQQLDQPGH
Retrocopy YQA*EEL*PMWDDLKAKIKQLLDEMLQFYHSQLDYIQHSFESLIRAQMVHYSEMLKIFGDLTQQLDQPGH

Parental  PDEQ
          PD.Q
Retrocopy PDKQ

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_1028 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005470	1 retrocopy	retro_btau_1291,
Macropus eugenii	ENSMEUG00000002173	1 retrocopy	retro_meug_545,
Myotis lucifugus	ENSMLUG00000005585	1 retrocopy	retro_mluc_1238,
Monodelphis domestica	ENSMODG00000009297	1 retrocopy	retro_mdom_346,
Pteropus vampyrus	ENSPVAG00000006191	1 retrocopy	retro_pvam_1028 ,