RetrogeneDB ID: retro_meug_1918

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold72182:12099..12685(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSMEUG00000014442
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_meug_1918
ATGGATAAAAATGAGCTGGTGCAGAAGGCCAAATTGGCTGAGCAGGCTGAGAGATATGATGACATGGCAGCCTGCATGAA
GTCTGTAACTGAGCAAGGAGCTGAATTATCCAATGAGGAGAGGAATCTTCTCTCTGTTGCTTACAAAAATGTCGTAGGGG
CCCGAAGGTCATCTTGGAGGGTTGTTTCAAGTATTGAGCAAAAGACGGAAGGTGCTGAGGAAAAAAAACAGCAGATGGCC
CGAGAATACAGAGAGAAAATTGAGACCGAACTAAGAGATATCTGCAATGATGTACTGTCTCTGTTGGAAAAGTTCTTGAT
TCCTAATGCTTCACAAGCAGAAAGCAAAGTTTTCTATTTGAAAATGAAAGGAGACTACTACCGTTATTTGGCTGAAGTTG
CTGCTGGTGATGACAAGAAAGGAATAGTGGATCAATCACAACAAGCATATCAAGAAGCATTTGAAATCAGCCAAAAGGAG
ATGCAACCCACGCATCCCTATAAGAATGGGTCTGGCTTTGAACTTCTCTGTGTTCTATTATGAGATCCTGAACTCTCCCC
AAAAAGCCTGCTCCCTTGCCAAGACA

Alignment

ORF - retro_meug_1918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 79.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEKTEMIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          M.K.E..QKAKLAEQAERYDDMA.CMK.VTEQGAELSNEERNLLSVAYKNVVG.RRS.WRV.SSIEQKT.
Retrocopy MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE

Parental  TSD-KKMQLVKDYXXXXXXXXXXXXXXXXELLDKFLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRK
          .......Q....Y.................LL.KFLI.NA...ESKVFYLKMKGDY.RYLAEVA.GDD.K
Retrocopy GAEXXXQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKK

Parental  QTIDNSQGAYQEAFDISKKEMQPTH-PIRLGLALNFSVFYYEILNNPELACTLAKT
          ...D.SQ.AYQEAF.IS.KEMQPTH.PIR.GLALNFSVFYYEILN.P..AC.LAKT
Retrocopy GIVDQSQQAYQEAFEISQKEMQPTH>PIRMGLALNFSVFYYEILNSPQKACSLAKT

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1918 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1918 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 9 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Macropus eugenii	ENSMEUG00000014442	7 retrocopies	retro_meug_1122, retro_meug_1208, retro_meug_1259, retro_meug_1549, retro_meug_1918 , retro_meug_2106, retro_meug_538,
Macropus eugenii	ENSMEUG00000015460	12 retrocopies	retro_meug_1290, retro_meug_1396, retro_meug_1536, retro_meug_16, retro_meug_1926, retro_meug_196, retro_meug_2153, retro_meug_2163, retro_meug_835, retro_meug_9, retro_meug_982, retro_meug_986,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pelodiscus sinensis	ENSPSIG00000012692	1 retrocopy	retro_psin_2,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,