RetrogeneDB ID: retro_meug_196

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_5685:77106..77809(-)
• Located in intron of: ENSMEUG00000002954

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSMEUG00000015460
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_meug_196
GATAAAAATGAGCTGGTGCAGAAGGCCAAATTGGCTGAGCAGGCTGAGAGATATGATGACATGGCAGCCTGCATGAAGTC
TGTAACTGAGCAAGAAGCTGAATTATCCAATGACGAGATGAATCTTCTCTCTGTTGCTTACAAAAATGTCATAGGGGCCC
AAAGGTCATCTTGGAGGGTTGTATTCAAATATTAAGCAAAAGAGGGAAGGTGCTGAGAAAAAACAGCAGATGGCCCGAGA
ATACAGAGAGAAAACTGAGATCGAACTAAGAGATATCTGCAATGATGTACTGTCTCTATTGGAAAAGTTCTTGACTCCTA
ATGCTTCACAAGCAGAAAGCAAAGTTTTCTATTTGAAAATGAAAGGAGAACACTATCGTTATTTGGCTGAGGTTGCTGCT
GGTGATGACAAGAAAGAAATAGTGCATCAATCCCAACAAGCATATCAAGAAGCATGTGAAATTAGCAAAAAGGAGATACA
ACCAACACATCCTGTAAGACTTGGTCTGGCTTTGAACTTCTCTGTGTTCTATTAGGAGATCCTGAACTCTCCAGAGAAAG
CCTGCTCCCTTGCAAAGACAGCTTTGGATGAAGCCATTGCTGAGCTTCATACATTAAATGAAGAATCATACAAAGACAGC
ACATTAATAATGCAGTTACTGAGAGACAACTTGACATTGTGGACATCAGATACCCAAGGAGAT

Alignment

ORF - retro_meug_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.14 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DREDLVYQAKLAEQAERYD-MVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRII-SSIEQKEE
          D...LV..AKLAEQAERYD.M...MK.V.....EL...E.NLLSVAYKNVIGA.R.SWR...S.I.QK.E
Retrocopy DKNELVQKAKLAEQAERYDDMAACMKSVTEQEAELSNDEMNLLSVAYKNVIGAQRSSWRVV>SNIKQKRE

Parental  NKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDR
          ..G.E.K..M.REYR...E.EL..IC.D.L..L.K.L.P.A...ESKVFY.KMKG...RYLAE.A.G.D.
Retrocopy --GAEKKQQMAREYREKTEIELRDICNDVLSLLEKFLTPNASQAESKVFYLKMKGEHYRYLAEVAAGDDK

Parental  KEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSE
          KE....S..AY..A..I...E..PTHP.RLGLALNFSVFY.EILNSP..AC.LAK.A.D.AIAEL.TL.E
Retrocopy KEIVHQSQQAYQEACEISKKEIQPTHPVRLGLALNFSVFY*EILNSPEKACSLAKTALDEAIAELHTLNE

Parental  ESYKDSTLIMQLLRDNLTLWTSDMQGD
          ESYKDSTLIMQLLRDNLTLWTSD.QGD
Retrocopy ESYKDSTLIMQLLRDNLTLWTSDTQGD

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_196 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_196 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 6 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
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,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,