RetrogeneDB ID: retro_dnov_339

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3795:110264..110615(+)
• Located in intron of: ENSDNOG00000011170

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSDNOG00000011179
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_dnov_339
ATGGTCCAGTGTTTGACATACTGTCGTAGGCTATGCTACAAAAGTGCCTCTAGCAAAACTAGGCTGTCCAGGACCCCTGG
TCATAGAATTATTTGCCTTTGTATCAGTGAAGTTGGGAAAGCACCAAAATCTGTTTGTGGTGTATGCCCAGGTCGACTGT
GGGGAGTTCATGCTGTGAGACCTAAAGTTCTTAGAAGGTTATCCAAAACAAAAAAACATGTCAGCAGAGCCTATGGTGGT
TCCATATGTGCTAAATGTGTCTGTGACAGGATCAAGCTTGCTTTTCTGATTGAGGAACAGAAAATCATTGTGAAAGTGCT
GAAAGCACAAGCACAGAGTCAGAAAGTTAAA

Alignment

ORF - retro_dnov_339 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKT
          MVQ.LTY.RRL.Y..AS.KTRLSRTPG.RI..L....VGKAPKS.CGVCPGRL.GV.AVRPKVL.RLSKT
Retrocopy MVQCLTYCRRLCYKSASSKTRLSRTPGHRIICLCISEVGKAPKSVCGVCPGRLWGVHAVRPKVLRRLSKT

Parental  KKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
          KKHVSRAYGGS.CAKCV.DRIK.AFLIEEQKI.VKVLKAQAQSQK.K
Retrocopy KKHVSRAYGGSICAKCVCDRIKLAFLIEEQKIIVKVLKAQAQSQKVK

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
SRP012922_ascending_colon	0.19 RPM	104.23 RPM
SRP012922_cerebellum	0.00 RPM	55.81 RPM
SRP012922_heart	0.00 RPM	69.38 RPM
SRP012922_kidney	0.55 RPM	133.06 RPM
SRP012922_liver	0.00 RPM	60.84 RPM
SRP012922_lung	0.00 RPM	161.28 RPM
SRP012922_quadricep_muscle	0.00 RPM	78.41 RPM
SRP012922_spleen	0.00 RPM	168.03 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_339 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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.

---

Parental genes homology:

Parental genes homology involve 36 parental genes, and 473 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001758	20 retrocopies	retro_amel_1151, retro_amel_1298, retro_amel_1402, retro_amel_147, retro_amel_1595, retro_amel_1670, retro_amel_1678, retro_amel_1755, retro_amel_240, retro_amel_368, retro_amel_388, retro_amel_410, retro_amel_477, retro_amel_655, retro_amel_690, retro_amel_739, retro_amel_874, retro_amel_936, retro_amel_949, retro_amel_978,
Bos taurus	ENSBTAG00000014226	13 retrocopies	retro_btau_1017, retro_btau_1141, retro_btau_1280, retro_btau_1303, retro_btau_1372, retro_btau_1476, retro_btau_1738, retro_btau_288, retro_btau_404, retro_btau_465, retro_btau_628, retro_btau_712, retro_btau_904,
Callithrix jacchus	ENSCJAG00000015993	4 retrocopies	retro_cjac_130, retro_cjac_293, retro_cjac_83, retro_cjac_99,
Cavia porcellus	ENSCPOG00000000802	6 retrocopies	retro_cpor_139, retro_cpor_1494, retro_cpor_402, retro_cpor_485, retro_cpor_694, retro_cpor_732,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339 , retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Equus caballus	ENSECAG00000019719	1 retrocopy	retro_ecab_58,
Erinaceus europaeus	ENSEEUG00000010390	5 retrocopies	retro_eeur_169, retro_eeur_175, retro_eeur_373, retro_eeur_82, retro_eeur_89,
Felis catus	ENSFCAG00000015502	16 retrocopies	retro_fcat_1240, retro_fcat_1334, retro_fcat_1401, retro_fcat_1453, retro_fcat_1492, retro_fcat_1508, retro_fcat_1619, retro_fcat_2010, retro_fcat_368, retro_fcat_434, retro_fcat_518, retro_fcat_544, retro_fcat_640, retro_fcat_941, retro_fcat_953, retro_fcat_956,
Homo sapiens	ENSG00000109475	33 retrocopies	retro_hsap_1245, retro_hsap_126, retro_hsap_1265, retro_hsap_1417, retro_hsap_1636, retro_hsap_1735, retro_hsap_1756, retro_hsap_1921, retro_hsap_1987, retro_hsap_2041, retro_hsap_2145, retro_hsap_232, retro_hsap_2570, retro_hsap_258, retro_hsap_2624, retro_hsap_2695, retro_hsap_288, retro_hsap_2997, retro_hsap_3090, retro_hsap_3463, retro_hsap_3550, retro_hsap_3689, retro_hsap_4055, retro_hsap_4091, retro_hsap_4314, retro_hsap_520, retro_hsap_720, retro_hsap_769, retro_hsap_830, retro_hsap_853, retro_hsap_927, retro_hsap_941, retro_hsap_977,
Gorilla gorilla	ENSGGOG00000007650	32 retrocopies	retro_ggor_1097, retro_ggor_1236, retro_ggor_1401, retro_ggor_1471, retro_ggor_1604, retro_ggor_1657, retro_ggor_1878, retro_ggor_2123, retro_ggor_2249, retro_ggor_226, retro_ggor_2262, retro_ggor_2336, retro_ggor_2397, retro_ggor_2494, retro_ggor_2723, retro_ggor_2744, retro_ggor_2884, retro_ggor_3042, retro_ggor_308, retro_ggor_327, retro_ggor_462, retro_ggor_479, retro_ggor_561, retro_ggor_607, retro_ggor_638, retro_ggor_680, retro_ggor_696, retro_ggor_747, retro_ggor_760, retro_ggor_781, retro_ggor_975, retro_ggor_995,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Microcebus murinus	ENSMICG00000002180	32 retrocopies	retro_mmur_1029, retro_mmur_1274, retro_mmur_1302, retro_mmur_1328, retro_mmur_134, retro_mmur_1366, retro_mmur_1412, retro_mmur_1424, retro_mmur_147, retro_mmur_1495, retro_mmur_1541, retro_mmur_187, retro_mmur_221, retro_mmur_286, retro_mmur_309, retro_mmur_336, retro_mmur_417,