RetrogeneDB ID: retro_mdom_1659

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:71616749..71617121(-)
• Located in intron of: ENSMODG00000024991

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS15A
• Ensembl ID: ENSMODG00000005920
• Aliases: None
• Description: ribosomal protein S15a [Source:HGNC Symbol;Acc:10389]

Sequence

>retro_mdom_1659
GTGGTGCACATGAATGTCCTGGCAAATGCTCTCAGAAGCATCGACAATTTGAGGAAAAGCCAGGTTCTTATTATACCATG
TTCTAAAGTAATTGTTCAGTTCCTAACTGTGCTTCTGTCATCACAGTTACATTGGCAAATGTGAAATCATCAATGATCAC
AGAGCAGGAAAAATGGATGTAAACTCATGAGCAGATTAAACAAGTGTGCTGTAATCAGCTCCAGATCGGATATTCAACTG
AAAGATCTGGAAAAGTGGCAGAATAATTGGCTGCTGTCCTGTCAGTTTGGGTTCATTGTGCCTACAACCTCAGTTGGTAT
CCCGGATCATAGATGAAAACACAGAGGAGAAAAAATCCTGGGATTCTTTTTT

Alignment

ORF - retro_mdom_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMK-HGYIGEFEIIDDHRAGKIVVN-LTGR
          .V.MNVLA.AL.SI.N.....K.QVLI.PCSKVIV.FLTV....H.YIG..EII.DHRAGK..VN.L..R
Retrocopy VVHMNVLANALRSIDNLR---KSQVLIIPCSKVIVQFLTVLLS>HSYIGKCEIINDHRAGKMDVN<LMSR

Parental  LNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF
          LNKC.VIS.R.D.QLKDLEKWQNN.L.S.QFGFIV.TTS.GI.DH...R.KH.G.KILGFFF
Retrocopy LNKCAVISSRSDIQLKDLEKWQNNWLLSCQFGFIVPTTSVGIPDH---R*KHRGEKILGFFF

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_1659 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1659 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 12 parental genes, and 168 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020733	5 retrocopies	retro_btau_14, retro_btau_171, retro_btau_3, retro_btau_57, retro_btau_98,
Callithrix jacchus	ENSCJAG00000020071	6 retrocopies	retro_cjac_120, retro_cjac_128, retro_cjac_170, retro_cjac_231, retro_cjac_359, retro_cjac_80,
Gadus morhua	ENSGMOG00000005862	1 retrocopy	retro_gmor_16,
Latimeria chalumnae	ENSLACG00000011476	1 retrocopy	retro_lcha_55,
Loxodonta africana	ENSLAFG00000026996	13 retrocopies	retro_lafr_1161, retro_lafr_1201, retro_lafr_210, retro_lafr_236, retro_lafr_247, retro_lafr_309, retro_lafr_323, retro_lafr_356, retro_lafr_571, retro_lafr_613, retro_lafr_629, retro_lafr_759, retro_lafr_956,
Macropus eugenii	ENSMEUG00000003956	14 retrocopies	retro_meug_1163, retro_meug_1214, retro_meug_1344, retro_meug_1582, retro_meug_1675, retro_meug_1803, retro_meug_184, retro_meug_1845, retro_meug_195, retro_meug_2169, retro_meug_340, retro_meug_520, retro_meug_729, retro_meug_809,
Myotis lucifugus	ENSMLUG00000005660	15 retrocopies	retro_mluc_1170, retro_mluc_1376, retro_mluc_1408, retro_mluc_1692, retro_mluc_2038, retro_mluc_2242, retro_mluc_2353, retro_mluc_2406, retro_mluc_2465, retro_mluc_2512, retro_mluc_2514, retro_mluc_263, retro_mluc_823, retro_mluc_824, retro_mluc_949,
Monodelphis domestica	ENSMODG00000005920	6 retrocopies	retro_mdom_1147, retro_mdom_1626, retro_mdom_1659 , retro_mdom_1852, retro_mdom_717, retro_mdom_83,
Otolemur garnettii	ENSOGAG00000013199	14 retrocopies	retro_ogar_102, retro_ogar_1254, retro_ogar_1302, retro_ogar_1361, retro_ogar_1636, retro_ogar_2241, retro_ogar_2361, retro_ogar_269, retro_ogar_2775, retro_ogar_3283, retro_ogar_3367, retro_ogar_563, retro_ogar_712, retro_ogar_87,
Pan troglodytes	ENSPTRG00000007823	2 retrocopies	retro_ptro_289, retro_ptro_76,
Rattus norvegicus	ENSRNOG00000018320	5 retrocopies	retro_rnor_1808, retro_rnor_2080, retro_rnor_2586, retro_rnor_324, retro_rnor_378,
Tupaia belangeri	ENSTBEG00000013626	86 retrocopies	retro_tbel_1030, retro_tbel_1045, retro_tbel_1051, retro_tbel_1075, retro_tbel_1079, retro_tbel_1087, retro_tbel_1100, retro_tbel_1111, retro_tbel_1118, retro_tbel_1222, retro_tbel_1284, retro_tbel_1371, retro_tbel_1398, retro_tbel_143, retro_tbel_1431, retro_tbel_1436, retro_tbel_1470, retro_tbel_1499, retro_tbel_155, retro_tbel_1561, retro_tbel_1625, retro_tbel_1709, retro_tbel_1800, retro_tbel_1842, retro_tbel_1886, retro_tbel_1970, retro_tbel_1975, retro_tbel_1976, retro_tbel_2318, retro_tbel_235, retro_tbel_2394, retro_tbel_2395, retro_tbel_2403, retro_tbel_2552, retro_tbel_2656, retro_tbel_2686, retro_tbel_2734, retro_tbel_2779, retro_tbel_2794, retro_tbel_2871, retro_tbel_2904, retro_tbel_2909, retro_tbel_2921, retro_tbel_2977, retro_tbel_2982, retro_tbel_299, retro_tbel_2990, retro_tbel_3074, retro_tbel_3087, retro_tbel_3173, retro_tbel_3237, retro_tbel_3419, retro_tbel_3428, retro_tbel_3489, retro_tbel_3498, retro_tbel_3562, retro_tbel_3610, retro_tbel_3657, retro_tbel_3752, retro_tbel_3761, retro_tbel_379, retro_tbel_3791, retro_tbel_382, retro_tbel_3884, retro_tbel_4084, retro_tbel_4195, retro_tbel_4198, retro_tbel_4210, retro_tbel_4550, retro_tbel_4584, retro_tbel_4605, retro_tbel_4626, retro_tbel_4707, retro_tbel_477, retro_tbel_479, retro_tbel_501, retro_tbel_547, retro_tbel_641, retro_tbel_646, retro_tbel_713, retro_tbel_774, retro_tbel_78, retro_tbel_806, retro_tbel_813, retro_tbel_862, retro_tbel_989,