RetrogeneDB ID: retro_pvam_699

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_83:64749..65417(-)
• Located in intron of: ENSPVAG00000017861

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32B
• Ensembl ID: ENSPVAG00000006569
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member B [Source:HGNC Symbol;Acc:16677]

Sequence

>retro_pvam_699
ACGCCCCCTGATGTGAAAGGGCTTGTCCTGGACAACTGCCACTCAAACGAGGGCAAAATCGAAGGCCTCACAGACGAATG
TGAAGAACTGGAGTTCTTAAGTATGATCAACGTAGGCCTCGCCTCAGTCTGCAAACTTACCGAAGCTAAACAAACTTAAG
AAGCTTGAACTAAGTGATAAGAGAATCTCGGGAGGCCTGGAAGTATTGGCAGAAGTGCCTGAACCTCACACATCTAAATG
TAAGTGGCAACAAAATTAAAGACCTCAGCGCAACAGAGCCACTGAATAAGTTAGAAAACCTCAAGAACTTAGACCTTTTC
AGTTGTGAAGTAACCACCCTGAATGACTACTGAGAAAAGCTGTTTAAGCTCCTCCCACAACTCACATACCTCAATGGCCA
CAGCCAGGATGACAAGGAGGCCCCTGGCTCAGACGCGGAGGGCTATGCAGAGGGCCTGGATGACAACGAGGAGGACGAGG
AAGCATATGATGAGGATGCTCAGGTGGTGGAGGAAGGTGAAGAGGAGGATGTGAGTGGAGAGGAAGAGGAAGATGAAGGA
GGTTATAACAACAGGGAAGTAGACGATAAGGAAGATGAAGATCTTGGTGTAAAGGAAAGAGGTCAGAAGTGAAAACGAGA
ACCTGAAGATGAGGGAGAAGATGACGAC

Alignment

ORF - retro_pvam_699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.44 %
• Parental protein coverage: 85.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSDNRIYGGLDML
          TP..V..LVLDNC.SN.GKIEGLT.E...LEFLS.INVGL.SV..NLPKL.KLKKLELSD.RI.GGL..L
Retrocopy TPPDVKGLVLDNCHSNEGKIEGLTDECEELEFLSMINVGLASV>ANLPKLNKLKKLELSDKRISGGLEVL

Parental  AEKLP-NLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDRED
          AE..P.NLTHLN.SGNK.KD.S..EPL.KLE.LK.LDLF.CEVT.LNDY.E..FKLLPQLTYL.G....D
Retrocopy AE-VP>NLTHLNVSGNKIKDLSATEPLNKLENLKNLDLFSCEVTTLNDY*EKLFKLLPQLTYLNGHSQDD

Parental  REAPDSDAE--VDGVDEEEDDEEGEDEEDEDDEDGEDEEFDDEEDEDE----DDDVEGEEDED-EVSGED
          .EAP.SDAE....G.D..E.DEE..DE.....E.GE.E....EE.EDE.......V...EDED..V....
Retrocopy KEAPGSDAEGYAEGLDDNEEDEEAYDEDAQVVEEGEEEDVSGEEEEDEGGYNNREVDDKEDEDLGVKERG

Parental  EDFGHDGEDEDEDED
          .......EDE.ED.D
Retrocopy QK*KREPEDEGEDDD

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_699 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 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246, retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399,
Nomascus leucogenys	ENSNLEG00000016941	1 retrocopy	retro_nleu_3009,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699 ,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,