RetrogeneDB ID: retro_amel_1837

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194696.1:129224..129949(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSAMEG00000008618
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_amel_1837
AAGAAGACAGAGCTCATCTAGAAGGTGAAGCTGGCTGACCTGGCCAAGCGCTACGACAACGTGGCAATTTGCATAAAGGC
CAAGACTGAGCAGGGTGCCAAGCTGTGAAAAAAGGAGAGAAACCCACTCTCAGTGGCCTACACAAATGTGGCTGGGGCTG
AAGGTCAGCGTGGAGGGTCATCTGGAACGTGGAGCTGAAAACTGACACCTCCAACAAGAAGTTGGACAGCTTATTAAGGA
CTATTGGAGAAAGTGGAGTCTGAACTGAGATCCATCTGTATCACAGTATTGGAATTGTTGGACAAGTATTTAATAGCCAA
TGAGACTAATCCAGAGAGTAAGGTCTTTTATCTGAAAATGAAGGGAGATTACTTGAGGTACTTTGTTGAAGTGGCATGTG
ATGATAATCAAAAACAAACAATAGATAATTCCCAAGGAGCTTACCAAGAGGCTTTTGATATAAGCAAGAAAGAGATGCAA
CCTCTATACCCAATCTGCCTGCGGCTGGCTCTTAATGTTTCTGTATTTTACTATGAGATCCTTAATAACCCAGAGCTTGC
CCGCACCCTGGCTCAAACTGCTTTTGATGAGGACATTGCAGAACTTGATAGACCGAATGAAGACTCATGCAAAGACAGCA
CCCTATCATGTAGTTGCTTAGAGACAACCTAACATTATGGACATCAGACAGTGCAGAAGAAGAATGTGATGCATCAGAAG
GGGCA

Alignment

ORF - retro_amel_1837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EKTELIQKAKLAKQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVG-GRRSAWRVISSIEQKTD
          .KTELI.K.KLA..A.RYD..A.C.KA.TEQGA.L...ERN.LSVAY.NV.G.G.RSAWRVI...E.KTD
Retrocopy KKTELI*KVKLADLAKRYDNVAICIKAKTEQGAKL*KKERNPLSVAYTNVAG<G*RSAWRVIWNVELKTD

Parental  TSDKKL-QLIK-DYREK-VESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDD
          TS.KKL..L...DY..K.VESELRSIC.TVLELLDKYLIAN.TNPESKVFYLKMKGDY.RY..EVAC.D.
Retrocopy TSNKKLDSLLR<DYWRK<VESELRSICITVLELLDKYLIANETNPESKVFYLKMKGDYLRYFVEVACDDN

Parental  RKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLN
          .KQTIDNSQGAYQEAFDISKKEMQP..PI.L.LALN.SVFYYEILNNPELA.TLA.TAFDE.IAELD..N
Retrocopy QKQTIDNSQGAYQEAFDISKKEMQPLYPICLRLALNVSVFYYEILNNPELARTLAQTAFDEDIAELDRPN

Parental  EDSYKDSTL-IMQLLRDNLTLWTSDSAGEECDVAEGA
          EDS.KDSTL.IM.LLRDNLTLWTSDSA.EECD..EGA
Retrocopy EDSCKDSTL<IM*LLRDNLTLWTSDSAEEECDASEGA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1837 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1837 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 10 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000328	1 retrocopy	retro_amel_562,
Ailuropoda melanoleuca	ENSAMEG00000008618	4 retrocopies	retro_amel_1214, retro_amel_1382, retro_amel_1837 , retro_amel_917,
Cavia porcellus	ENSCPOG00000011321	4 retrocopies	retro_cpor_135, retro_cpor_1463, retro_cpor_616, retro_cpor_668,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
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,