RetrogeneDB ID: retro_mdom_1878

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:203870030..203870324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025578
• Aliases: None
• Description: None

Sequence

>retro_mdom_1878
AGAAGGCTCTAGGATAGGAAGCAGAGTGTCTATGGTGGTCAGACCAAACCAATTTTCAGGAAAAAGGCAGAAACCACGAA
AAAGATTGTACTGAGGCTTGAATATTTGGAACCCAGCTGCATGACAAAAAGGATGCTTTCCATTAAGAGGTGTATTTTGA
ACTGGGAGGAAGTAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTGAGTTTCACTGTTTTTGTCTTAACAGAAAAAACCAT
TCCATTCCATCCCTTGGTTTTGTATCTTCTGTCTTGGAAAGGAAAAGGCTTGAA

Alignment

ORF - retro_mdom_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.47 %
• Parental protein coverage: 72.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRLYDRKQSGYGGQTKPIFRKKAETTKRVVLRLECLGPSCRTKRMLAIKRC-KRFELGRSKKRKGQVIQF
          RRL.DRKQS.YGGQTKPIFRKKAETTK..VLRLE.L.PSC.TKRML.IKRC....E..R....K.....F
Retrocopy RRL*DRKQSVYGGQTKPIFRKKAETTKKIVLRLEYLEPSCMTKRMLSIKRCILNWEEVRRERAK*SSSEF

Parental  HCFRLDRKNHSIPSLGFVFSVLERKRLE
          HCF.L.RKNHSIPSLGFV.SVLERKRLE
Retrocopy HCFCLNRKNHSIPSLGFVSSVLERKRLE

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_1878 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1878 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 26 parental genes, and 178 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Ailuropoda melanoleuca	ENSAMEG00000009384	1 retrocopy	retro_amel_85,
Bos taurus	ENSBTAG00000019253	3 retrocopies	retro_btau_183, retro_btau_241, retro_btau_92,
Canis familiaris	ENSCAFG00000017688	1 retrocopy	retro_cfam_154,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Dasypus novemcinctus	ENSDNOG00000015954	23 retrocopies	retro_dnov_1206, retro_dnov_1266, retro_dnov_1320, retro_dnov_1328, retro_dnov_1330, retro_dnov_1392, retro_dnov_1427, retro_dnov_1525, retro_dnov_1799, retro_dnov_1898, retro_dnov_227, retro_dnov_2302, retro_dnov_233, retro_dnov_2371, retro_dnov_243, retro_dnov_2488, retro_dnov_2503, retro_dnov_2587, retro_dnov_310, retro_dnov_596, retro_dnov_699, retro_dnov_871, retro_dnov_936,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Felis catus	ENSFCAG00000015397	3 retrocopies	retro_fcat_106, retro_fcat_25, retro_fcat_80,
Homo sapiens	ENSG00000241343	14 retrocopies	retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2, retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Homo sapiens	ENSG00000257529	1 retrocopy	retro_hsap_1353,
Gorilla gorilla	ENSGGOG00000009460	6 retrocopies	retro_ggor_13, retro_ggor_152, retro_ggor_207, retro_ggor_208, retro_ggor_42, retro_ggor_5,
Loxodonta africana	ENSLAFG00000017385	1 retrocopy	retro_lafr_114,
Macropus eugenii	ENSMEUG00000014912	6 retrocopies	retro_meug_1056, retro_meug_1381, retro_meug_1610, retro_meug_1979, retro_meug_2185, retro_meug_489,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878 , retro_mdom_971,
Mustela putorius furo	ENSMPUG00000002168	3 retrocopies	retro_mputfur_269, retro_mputfur_530, retro_mputfur_94,
Mus musculus	ENSMUSG00000079435	1 retrocopy	retro_mmus_4,
Nomascus leucogenys	ENSNLEG00000007540	27 retrocopies	retro_nleu_1003, retro_nleu_1243, retro_nleu_1291, retro_nleu_153, retro_nleu_157, retro_nleu_1632, retro_nleu_178, retro_nleu_1833, retro_nleu_1903, retro_nleu_1959, retro_nleu_2145, retro_nleu_2345, retro_nleu_2381, retro_nleu_2699, retro_nleu_2965, retro_nleu_2995, retro_nleu_2996, retro_nleu_3027, retro_nleu_3028, retro_nleu_3059, retro_nleu_3111, retro_nleu_385, retro_nleu_453, retro_nleu_644, retro_nleu_805, retro_nleu_842, retro_nleu_991,
Otolemur garnettii	ENSOGAG00000004551	6 retrocopies	retro_ogar_1160, retro_ogar_1681, retro_ogar_2390, retro_ogar_2519, retro_ogar_294, retro_ogar_470,
Pongo abelii	ENSPPYG00000025837	37 retrocopies	retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011, retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sorex araneus	ENSSARG00000014178	4 retrocopies	retro_sara_146, retro_sara_488, retro_sara_617, retro_sara_76,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Ictidomys tridecemlineatus	ENSSTOG00000027251	20 retrocopies	retro_itri_1171, retro_itri_1189, retro_itri_1364, retro_itri_1405, retro_itri_1471, retro_itri_161, retro_itri_1681, retro_itri_290, retro_itri_385, retro_itri_430, retro_itri_555, retro_itri_609, retro_itri_644, retro_itri_730, retro_itri_753, retro_itri_784, retro_itri_803, retro_itri_845, retro_itri_865, retro_itri_903,
Tupaia belangeri	ENSTBEG00000015808	1 retrocopy	retro_tbel_52,
Tursiops truncatus	ENSTTRG00000012779	1 retrocopy	retro_ttru_5,