RetrogeneDB ID: retro_meug_246

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_7586:105589..106074(+)
• Located in intron of: ENSMEUG00000015593

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSMEUG00000007909
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A/B [Source:HGNC Symbol;Acc:5034]

Sequence

>retro_meug_246
AAGAAAGATCTCACTGATACCTGTCTCCTTTTACAGAGGTTGTAGACTGCACAATTAAAACAGATTCCTTCATGGGAAGA
TCAAGGGAATTCAGATTTGTGCTTTTTAAAGATGCTACCAGTGTCAATGAATCTTGAAACTTAAAGAACACAAGCTGGGT
GGCAAGTTGATAGACTTCAAAAGGGTCAAAAAGCTTTAAAGGGAAAGAAGCCCTCTAAGAAGGTGTTTGTTGGTGGACTG
AACCCAGATCCATTTGAAGAACAAATCAAAGAATATTTTGGAGCATTGAGTGAGATTGAAAATATTGAACTATGGGCACA
AAAACAAATGAAAGAAGAGGATTTTGTTTTATCACATATATAGAACCAGTAAAGAAATTATTAGAAAACAGATATCATCA
GATTGGTTTGGGGAAGTGTGAAATCAAAGTTGCCCAACGCAAAGAGCTATACAGGCAGTCACCAAAACAACAAAAAGGAG
GGAGG

Alignment

ORF - retro_meug_246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.76 %
• Parental protein coverage: 57.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKDLKD-YFTKFGEVVDCTIKMDPNTGRSRGFGFILFKESASVDK-VLDQKEHRLDGRVIDPKKAMAM--
          KKDL.D.Y...F.EVVDCTIK.D...GRSR.F.F.LFK...SV....L..KEH.L.G..ID.K.......
Retrocopy KKDLTD<YLSPFTEVVDCTIKTDSFMGRSREFRFVLFKDATSVNE<ILKLKEHKLGGKLIDFKRVKKL*R

Parental  KKDPV-KKIFVGGLNPEATEDKIREYFGDFGEIESIELPMDPKTNKRRGFV-FITFKEEDPVKKILEKKF
          ...P..KK.FVGGLNP...E..I.EYFG...EIE.IEL....K..K...FV.FIT..E..PVKK.LE...
Retrocopy ERSPL<KKVFVGGLNPDPFEEQIKEYFGALSEIENIEL-WAQKQMKEEDFV<FITYIE--PVKKLLENRY

Parental  HNVGGSKCEIKVAQPKEVYQQQQYSSGGSR
          H..G..KCEIKVAQ.KE.Y.Q......G.R
Retrocopy HQIGLGKCEIKVAQRKELYRQSPKQQKGGR

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_246 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_246 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246 ,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,