RetrogeneDB ID: retro_meug_56

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_10170:18879..19589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSMEUG00000013622
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_meug_56
CAAACACTCCAGGGGCTTTGGTTTTGCTACCTATGCCACAGTGCAAGAGGTAGATGCAATCATGAATGAATGAAAGACCT
CACAAAATTGATGACAGAGTTGTTGAACCAAAGAGAGTTGTTTCCAGAGGGAACATTCAAAGGCCAGGTGCCCACTTAAC
TGTGAAAAAGATCTTTATGGGTGGCAGTAAGGAAGACAGAGAAGAATCACTTAAGAGACTATTTTGAACAATATAGAAAA
ATTGAAGTGATTGAAATCATGACTAACCAAGGCAGGGGCAAAAAGAGAGGCTTTGCTTTCATTATTTTGGATGACCATGA
TTCTGTGGATAAGATTGTCACTCAAAAATATCATACTGTGAATGGCCACAACTGTGAAGTAAGGAAAGCTTTGTTTAAGA
AGAAATGGCCAGCACTTCATCTAGTCAAAGAGGTCAAAGTGGTTCTAGAAACCTTAGCAGTGGCCATGGAGGTGGCTTTG
GTGGAAATGATAACTTTGGCCATGGTGGGAACTTCAGTGGTTGAGATTATTTTGGCAGTGGTTATGGTGGTGGAGGATAT
GGTGGACGTGGAGATGGCTACAATGGATTTGGAAATGATGGAAGAAACCTTGGAGTTGGTGGGAACTACAATGATTTTGG
CAACTATAATAATCAGTCTTCAAACTTTGGTCTGGTGAAGGGAAGAAACTTTGGAGGGAGGAGCTCAGGT

Alignment

ORF - retro_meug_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.28 %
• Parental protein coverage: 63.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTKRSRGFGFVTYS-CVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEE
          QT.....F.....S.C.......M..RPHK.D.RVVEPKR.VSR.....PGAHLTVKKIF.GG.KED.EE
Retrocopy QTLQGLWFCYLCHS<CKR*MQS*MNERPHKIDDRVVEPKRVVSRGNIQRPGAHLTVKKIFMGGSKEDREE

Parental  YNLRDYF-EKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSK-QEM
          ..L...F.E.Y.KIE.IE.M.....GKKRGFAF...DDHD.VDKIV.QKYHT.NGHNCEV.KAL.K..EM
Retrocopy -SLKRLF>EQYRKIEVIEIMTNQGRGKKRGFAFIILDDHDSVDKIVTQKYHTVNGHNCEVRKALFK<EEM

Parental  QS-AGSQRGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGN
          .S...SQRG..G......G.GG.F.GG..NFG.GGNF.G....G.G.GG..G.YGG...GYNGFG.DG.N
Retrocopy ASTSSSQRGQSGSRNLSSGHGGGF-GGNDNFGHGGNFSG*DYFGSGYGG--GGYGGRGDGYNGFGNDGRN

Parental  YGGGPGYSSRGGYGGGGGPGYGNQGGGYGGGGGG
          .G.G..Y...G.Y...........G...GG...G
Retrocopy LGVGGNYNDFGNYNNQSSNFGLVKGRNFGGRSSG

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_56 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_56 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 22 parental genes, and 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
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 ,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,