RetrogeneDB ID: retro_mdom_1464

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:178871310..178871662(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSMODG00000001704
• Aliases: None
• Description: ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]

Sequence

>retro_mdom_1464
ATGGCTTTCTCAAAGAAAGGTATAGAGAAAAAGAAAGAATGTTCTGTCATCATCAAAGTAATGATCAGAGAGTATAACAT
AAACAGTCACAAATGGATCTGTAGAGCCTTCAAAAAGCAATCTCTGCAGGAAATTCACAAACTTTCCCTGAAAGAAATAG
AAACTCCAGATGTATACATAGACACCAGACTCAACAAAGCTGTTTAGGTCAAAGTAATAAGCAACATTCCATAGCAGATG
CAAGTGTGACAAAACGAAGAAGAAAATTCATGGAACTAGCTCTATACATTGATTACTTATATGCTTTTCACCCACCACTT
TCAAAAGCTTACAGACCTTCAATGTGGATAAA

Alignment

ORF - retro_mdom_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.79 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
          MA..KKG.EKKK..S.I..V..REY.IN.HK.I....FKK.....L.EI.K...KE..TPDV.IDTRLNK
Retrocopy MAFSKKGIEKKKECSVIIKVMIREYNINSHKWICRA-FKKQS---LQEIHKLSLKEIETPDVYIDTRLNK

Parental  AVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVT-TFKSL-QTVNVDE
          AV..K.I.N.P....V......N....S.N.LYTL.TY...T..F..L.QT.NVD.
Retrocopy AV*VKVISNIP*QMQV*QNEEEN----SWN*LYTLITYMLFTHHFQKL>QTFNVDK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1464 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1464 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 21 parental genes, and 167 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Ailuropoda melanoleuca	ENSAMEG00000015647	2 retrocopies	retro_amel_12, retro_amel_222,
Bos taurus	ENSBTAG00000019701	9 retrocopies	retro_btau_1043, retro_btau_1100, retro_btau_1553, retro_btau_160, retro_btau_1777, retro_btau_1783, retro_btau_409, retro_btau_524, retro_btau_867,
Felis catus	ENSFCAG00000026430	13 retrocopies	retro_fcat_1420, retro_fcat_148, retro_fcat_17, retro_fcat_190, retro_fcat_1957, retro_fcat_2003, retro_fcat_251, retro_fcat_46, retro_fcat_466, retro_fcat_658, retro_fcat_725, retro_fcat_803, retro_fcat_881,
Gorilla gorilla	ENSGGOG00000006432	24 retrocopies	retro_ggor_1047, retro_ggor_113, retro_ggor_1442, retro_ggor_169, retro_ggor_1811, retro_ggor_1839, retro_ggor_192, retro_ggor_1971, retro_ggor_21, retro_ggor_2132, retro_ggor_2383, retro_ggor_2541, retro_ggor_2547, retro_ggor_2625, retro_ggor_2820, retro_ggor_442, retro_ggor_583, retro_ggor_655, retro_ggor_834, retro_ggor_84, retro_ggor_849, retro_ggor_874, retro_ggor_88, retro_ggor_997,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Loxodonta africana	ENSLAFG00000027873	12 retrocopies	retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245, retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Microcebus murinus	ENSMICG00000016059	15 retrocopies	retro_mmur_1018, retro_mmur_1028, retro_mmur_1080, retro_mmur_130, retro_mmur_1320, retro_mmur_1369, retro_mmur_1386, retro_mmur_1606, retro_mmur_1617, retro_mmur_476, retro_mmur_506, retro_mmur_538, retro_mmur_639, retro_mmur_796, retro_mmur_996,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Macaca mulatta	ENSMMUG00000009873	1 retrocopy	retro_mmul_340,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464 , retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Mustela putorius furo	ENSMPUG00000012197	2 retrocopies	retro_mputfur_50, retro_mputfur_71,
Nomascus leucogenys	ENSNLEG00000014444	2 retrocopies	retro_nleu_47, retro_nleu_530,
Oryctolagus cuniculus	ENSOCUG00000002392	9 retrocopies	retro_ocun_1070, retro_ocun_1074, retro_ocun_1161, retro_ocun_117, retro_ocun_1366, retro_ocun_206, retro_ocun_64, retro_ocun_941, retro_ocun_99,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Rattus norvegicus	ENSRNOG00000013508	8 retrocopies	retro_rnor_101, retro_rnor_152, retro_rnor_1809, retro_rnor_217, retro_rnor_22, retro_rnor_267, retro_rnor_277, retro_rnor_286,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,
Ictidomys tridecemlineatus	ENSSTOG00000010902	15 retrocopies	retro_itri_1068, retro_itri_1074, retro_itri_1077, retro_itri_1140, retro_itri_1142, retro_itri_1223, retro_itri_1467, retro_itri_1570, retro_itri_1634, retro_itri_1791, retro_itri_1900, retro_itri_298, retro_itri_450, retro_itri_680, retro_itri_76,