RetrogeneDB ID: retro_dnov_1664

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_25913:9215..9636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSDNOG00000004813
• Aliases: None
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_dnov_1664
GTTGAACCTTCGGATACAAGAGAAAATATGAAAGCCAAGATCCAGGATAAGGAAGGAATTCCTCCTGATCAGCAGAGACT
GATCTTTGCTGGCAAAGCAACTAGAAGATGGACATACTTTGTCTGACTACAACATTCAAAATGAGTCCACTCTTCATCTT
GTGTTGAGACTTCGTGGTGGTGCTAAGACAAGGAAGAAGAAGTCTTACACTACTCCCAAGAAGAATAAGCATAAGAGAAA
GAAGGTTAAGCTGGCTGTCCTGAAATATTATAAGGTGGATGAGAATGGCAAAATTAGTCACCTTTGTAGGGAGTGCCCTT
CAGATGAATGTGGTGCTGGAGTTTTTATGGCCAGCCACTTCGACAGACATTACTGTGGCAAGTGTTGTCTGACTTACTGC
TTCAACAAACCAGAAGACAAG

Alignment

ORF - retro_dnov_1664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK-QLEDGRTLSDYNIQKESTLHLVLRLRGGAKKRKKKSY
          VEPSDT.EN.KAKIQDKEGIPPDQQRLIFAGK.QLEDG.TLSDYNIQ.ESTLHLVLRLRGGAK.RKKKSY
Retrocopy VEPSDTRENMKAKIQDKEGIPPDQQRLIFAGK>QLEDGHTLSDYNIQNESTLHLVLRLRGGAKTRKKKSY

Parental  TTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPED
          TTPKKNKHKRKKVKLAVLKYYKVDENGKIS.L.RECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPED
Retrocopy TTPKKNKHKRKKVKLAVLKYYKVDENGKISHLCRECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPED

Parental  K
          K
Retrocopy K

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	56.20 RPM	237.06 RPM
SRP012922_cerebellum	35.60 RPM	193.69 RPM
SRP012922_heart	52.67 RPM	170.78 RPM
SRP012922_kidney	107.33 RPM	578.26 RPM
SRP012922_liver	29.41 RPM	126.32 RPM
SRP012922_lung	95.91 RPM	407.77 RPM
SRP012922_quadricep_muscle	50.54 RPM	192.47 RPM
SRP012922_spleen	105.42 RPM	444.11 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_1664 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.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Cavia porcellus	ENSCPOG00000005819	7 retrocopies	retro_cpor_1040, retro_cpor_1433, retro_cpor_406, retro_cpor_409, retro_cpor_502, retro_cpor_591, retro_cpor_990,
Dasypus novemcinctus	ENSDNOG00000004813	12 retrocopies	retro_dnov_131, retro_dnov_1340, retro_dnov_1432, retro_dnov_1558, retro_dnov_1664 , retro_dnov_2022, retro_dnov_2183, retro_dnov_2576, retro_dnov_2635, retro_dnov_491, retro_dnov_538, retro_dnov_771,
Erinaceus europaeus	ENSEEUG00000002329	9 retrocopies	retro_eeur_127, retro_eeur_143, retro_eeur_193, retro_eeur_283, retro_eeur_289, retro_eeur_308, retro_eeur_58, retro_eeur_629, retro_eeur_72,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,