RetrogeneDB ID: retro_pvam_389

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2896:73182..73808(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSPVAG00000011401
• Aliases: None
• Description: annexin A2 [Source:HGNC Symbol;Acc:537]

Sequence

>retro_pvam_389
ACTTCTTTCAAAATGTCTACTGTTCACGAAATTCTGTGCAAGCCCAGCTAGGAGGGCGATCACTCTACCCTCCCAAGTAC
ACATGGATCGGTCAAAGCCTACGCCACCTCCGATGCCGACTGGGATGCTCCGAACATTGAAACGGCCATCGAGACGAAAG
GCGTGGACGAGGTCAGCATCGTCAGCATTTTGACCATCCGCAGCAACGAACAGAGACAGGATATTGCCTTTGCGTGCAGA
GAGGGAGTAACAAGAAACTTGCTTCAGCACTGCGGTCAGCCTTGCCTGGCCACCCAGAGACAGAGATTTTGGGCCTTTTG
AAAACACCTGCTCAGTGGGATGCTTCGGAGCTGAAAGCCTTTATGAAGGGGCTAGGGACCGAGGAGGACTCTCTCACTGA
GATCATCTGCTCAAGGACCCACCGAGAGCTGCAGGAAATTAAGAGTCCACAGGGACATGCACAAGACTGATCTGGAGAAG
GACATTTTTTTTCCGACACGGCTGTTGACTTCTACAAGCTGATCGTTGCCCTCACGTAGGGTAGCAGAGCAGAAGATGGA
TCTGTCATCAGTTCTGAACTGATTGACCCAGGCGCCCGGGATCTCTGCGACGCTGGAGTGAAGAGA

Alignment

ORF - retro_pvam_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSFKMSTVHEIMCKLSLEGDHSTPPSAYGSVKAYTNFDADRDALNIETAIKTKGVDEVTIVNILTNRSNE
          .SFKMSTVHEI.CK.S.EGDHST.PS..GSVKAY...DAD.DA.NIETAI.TKGVDEV.IV.ILT.RSNE
Retrocopy TSFKMSTVHEILCKPS*EGDHSTLPSTHGSVKAYATSDADWDAPNIETAIETKGVDEVSIVSILTIRSNE

Parental  QRQDIAFA-YQRRTKKELPSALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSR
          QRQDIAFA..QR...K.L.SAL.SAL.GH.ET.ILGLLKTPAQ.DASELKA.MKGLGT.EDSL.EIICSR
Retrocopy QRQDIAFA<VQRGSNKKLASALRSALPGHPETEILGLLKTPAQWDASELKAFMKGLGTEEDSLTEIICSR

Parental  TNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGKRAKDGSVIDYELIDQDARDLYDAGVKR
          T..ELQEI............E.....DT..DF.KL.VAL..G.RA.DGSVI..ELID..ARDL.DAGVKR
Retrocopy THRELQEIKSPQGHAQD*SGEGXXXXDTAVDFYKLIVALT*GSRAEDGSVISSELIDPGARDLCDAGVKR

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_389 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 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028, retro_chof_1965, retro_chof_815,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Pteropus vampyrus	ENSPVAG00000006489	2 retrocopies	retro_pvam_536, retro_pvam_713,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389 ,
Pteropus vampyrus	ENSPVAG00000013001	1 retrocopy	retro_pvam_1365,