RetrogeneDB ID: retro_pvam_983

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_20703:11944..12621(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSPVAG00000005334
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_pvam_983
CTACGACAACGGGCCACCTGCGTGAAGAAGGCTTTGACACGGCAGGGCGCCGAGCTACCCAAGGAGGAGCGCAACCTGCT
CTCGGTGGCCTATAAGAAAGTGGTTGGGGGCCACAGGTCCGCCCAGAGGGTCAACAAGCATCCAGCAGAAAACCGATCCC
TCAAACAAAAAGTTGCAGCTGATTAAGGACTATCAGGAAGAAAGTGGAGTCTGAACCGAGGTCCACCTGCACCACCATCC
TGTCGCTGTAGGATAAGTATTTAATAGCCAACGCAACTAATCCAGAGAGAAAGGATTTCTATCTAAAAATGAAGGGAGAT
TACTTCCGGTACCTTGCTGAAGTTGCATGTGGCGATGATCTAAGACAAACTATATAGATAATTCCCAAAGAGCTTACCAA
GAGGCTTTTGATGCAAGCCAAGAAAAGGGTGAAACCACACCTAATTCGTCTGAGGCTGGCTCTTCACATTTCTGTATTTT
ACTATGAGATCTTTAATAACCCAGAGCTTGCCTTCACACTGGCTAAAAGGGCTCTTGATGAGGCTATTGTAGAACCTGAT
ATGCTGAGTGAAGACTCTTACAGAGACAGCACCCTCATTACGCAGTTGCTTAGAGACCACCTCACGTGGACATCAGACAG
CACAGGAGAACAATGTTATGTGGCAGAAGGAGAAGAA

Alignment

ORF - retro_pvam_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 93.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LYDNATCVKKALIRQGAELPKEERNLLSVAYKKVVGGHRSAQRVN-SIQQKTDPSNKKLQLIKDYRE-KV
          L...ATCVKKAL.RQGAELPKEERNLLSVAYKKVVGGHRSAQRVN.SIQQKTDPSNKKLQLIKDY.E.KV
Retrocopy LRQRATCVKKALTRQGAELPKEERNLLSVAYKKVVGGHRSAQRVN>SIQQKTDPSNKKLQLIKDYQE>KV

Parental  ESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDIS
          ESE.RS.CTT.L.L.DKYLIANATNPE.K.FYLKMKGDYFRYLAEVACGDD..QTI..............
Retrocopy ESEPRSTCTTILSL*DKYLIANATNPERKDFYLKMKGDYFRYLAEVACGDDLRQTI*IIPKELTKRLLMQ

Parental  KKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLT
          .K.....H.IRL.LAL..SVFYYEI.NNPELA.TLAK.A.DEAI.E.D.L.EDSY.DSTLI.QLLRD.LT
Retrocopy AKKRVKPHLIRLRLALHISVFYYEIFNNPELAFTLAKRALDEAIVEPDMLSEDSYRDSTLITQLLRDHLT

Parental  LWTSDSAGEECDAAEGAE
          .WTSDS.GE.C..AEG.E
Retrocopy -WTSDSTGEQCYVAEGEE

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_983 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 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983 ,
Pteropus vampyrus	ENSPVAG00000012662	1 retrocopy	retro_pvam_157,
Pteropus vampyrus	ENSPVAG00000016641	1 retrocopy	retro_pvam_1101,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,