RetrogeneDB ID: retro_pvam_148

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1626:565165..566021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSPVAG00000013182
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_pvam_148
GTGAAAATGATTCTAGAATTCCAGAAAATTTCAGTTCCCATCAGGAACCTACAAAAGTAGAAGAAATTATCTGTGGTCTT
ATCAAAGGAGGAGCTGTCAAACTTCAGAGAAAAATATACTTTGATATGACACTGAATAGATTTTCCTATAAAAGGAAAAG
ATGTCCAACATGTCATAATGTCATTGTCAACTGTAATCTGGTTTTAGGTGAATGTCAGAAAAAGTCATTGCAACTAAAAG
AAAAATATCATGCTACCGAAATTGATTCTGTTCTTACCATAGAAGAGAGTACCCTTATATGGTAGAATGGTACACTAAAT
CACACAGTTTGCTTGATGAACAGGCTTTACCGAAAGCTAAAATTAAAGAAATTGTGGCAGAATCTGACGTTTTGCTCAAG
GAAGGGTATGAGAATTTCTTTGATAAGCTTTGACAACACAGAATCCCTGTATTCATATTTTTGGCTGGTATTGGTAATAT
GCTAGAGGAGATTATCTGTCAAGCTGGTGTCTATTATCCAAATGTCGAAGTAGTTTCCAACTTCATGGATTTTGATGACG
GTGGGATGCTCAAAGGATTTAAAGGAGAATTTATTTGCATATTTAACAAACATGATGGCGCGTTGAAGAACACAGAATAT
TTCAATCAACTAAAAGACAATAGCAACATAACTCTGCTGGGAGACTCTCAAGGAAATTTAAGAATGGCAGATAGAGTGGC
CAATGTTGAATGCATTCTGAAAACTGGATATCTAAATGATAGAGTGGATGCACTTTTAGAAAAGTAAATGGACTCTTATG
ATATTGTTCTTGTAAAAGATGAATTATCGGAGGTAGCTAACTCTATCTTACAAAAA

Alignment

ORF - retro_pvam_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 85.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IEMMPELQKNSVRIKN-PTRVEEILCGLIKGGAVKLQIITDFDMTLSRFSYEGKRCPTCHNVIDNCKLVS
          ..M..E.QK.SV.I.N.PT.VEEI.CGLIKGGAVKLQ....FDMTL.RFSY..KRCPTCHNVI.NC.LV.
Retrocopy VKMILEFQKISVPIRN<PTKVEEIICGLIKGGAVKLQRKIYFDMTLNRFSYKRKRCPTCHNVIVNCNLVL

Parental  DECRKKLLQLKEKYYAIEIDPLLTVEE-KFPHMEEWYTKSHSLLVEQALPKDKLREIVAESDVMLKEGYE
          .EC.KK.LQLKEKY.A.EID..LT.EE...P.M.EWYTKSHSLL.EQALPK.K..EIVAESDV.LKEGYE
Retrocopy GECQKKSLQLKEKYHATEIDSVLTIEE<EYPYMVEWYTKSHSLLDEQALPKAKIKEIVAESDVLLKEGYE

Parental  KFFDRLQQHSVPVFIFSAGIGDVLEEIIRQAGVYYPNVKVVSNFMDFDDNGVLKGFKGELIHVFNKHDGA
          .FFD.L.QH..PVFIF.AGIG..LEEII.QAGVYYPNV.VVSNFMDFDD.G.LKGFKGE.I..FNKHDGA
Retrocopy NFFDKL*QHRIPVFIFLAGIGNMLEEIICQAGVYYPNVEVVSNFMDFDDGGMLKGFKGEFICIFNKHDGA

Parental  LKNTEYFSELKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKEETLE
          LKNTEYF..LKDNSNI.LLGDSQG.LRMAD.VANVE.ILK.GYLNDRVD.LLEK.MDSYDIVLVK.E..E
Retrocopy LKNTEYFNQLKDNSNITLLGDSQGNLRMADRVANVECILKTGYLNDRVDALLEK*MDSYDIVLVKDELSE

Parental  VANSILQK
          VANSILQK
Retrocopy VANSILQK

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_148 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000010634	1 retrocopy	retro_pvam_233,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148 , retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,