RetrogeneDB ID: retro_dnov_218

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2712:449170..449521(+)
• Located in intron of: ENSDNOG00000001924

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSDNOG00000008083
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_dnov_218
ATGGCTTCTCAGTCGCAGGGCATCCAGCAGCTCCTGCAGGCGGAGAAGCGCGCTGCTGAGAAGGTGTCCTAGGCTCGCAA
GCGAAAGAACCGGAGGCTGAAGCAGGCCAAAGAAGCAGCTCAGGCTGAAACTGAACAGTACCGCCTGCAGAGGGAGAAGG
AGTTCAAGGCCAAAGAAGCTGCAGCTCTGGGATCCCACGGCAGTTGTAGCACTGAAGTGGAGGAGACCCAGAAGAAAATG
ACTATCCTCCAGAACTACTTCCAGCAGAACAGGGATGAAGTTCTGGATAACCTTTTGGCCTTTGTCTGTGACATCCGACC
AGAAATCCATGAAAACTACTGCATAAATGGA

Alignment

ORF - retro_dnov_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGSCS
          MASQSQGIQQLLQAEKRAAEKVS.ARKRKNRRLKQAKE.AQAE.EQYRLQREKEFKAKEAAALGSHGSCS
Retrocopy MASQSQGIQQLLQAEKRAAEKVS*ARKRKNRRLKQAKEAAQAETEQYRLQREKEFKAKEAAALGSHGSCS

Parental  TEVEKETQEKMTILQNYFQQNRDEVLDNLLAFVCDIRPEIHENYRING
          TEVE.ETQ.KMTILQNYFQQNRDEVLDNLLAFVCDIRPEIHENY.ING
Retrocopy TEVE-ETQKKMTILQNYFQQNRDEVLDNLLAFVCDIRPEIHENYCING

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	80.70 RPM
SRP012922_cerebellum	0.27 RPM	119.05 RPM
SRP012922_heart	0.00 RPM	59.86 RPM
SRP012922_kidney	0.27 RPM	150.31 RPM
SRP012922_liver	0.00 RPM	54.03 RPM
SRP012922_lung	0.00 RPM	142.95 RPM
SRP012922_quadricep_muscle	0.35 RPM	70.10 RPM
SRP012922_spleen	0.00 RPM	144.68 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_218 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 27 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012509	3 retrocopies	retro_amel_1053, retro_amel_376, retro_amel_999,
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
Cavia porcellus	ENSCPOG00000000763	5 retrocopies	retro_cpor_1523, retro_cpor_204, retro_cpor_688, retro_cpor_742, retro_cpor_852,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218 , retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Equus caballus	ENSECAG00000011155	1 retrocopy	retro_ecab_816,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Felis catus	ENSFCAG00000000160	2 retrocopies	retro_fcat_1614, retro_fcat_402,
Homo sapiens	ENSG00000136888	3 retrocopies	retro_hsap_3198, retro_hsap_4049, retro_hsap_763,
Gorilla gorilla	ENSGGOG00000004011	4 retrocopies	retro_ggor_1331, retro_ggor_2215, retro_ggor_2717, retro_ggor_632,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Microcebus murinus	ENSMICG00000015368	3 retrocopies	retro_mmur_1217, retro_mmur_1259, retro_mmur_755,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,