RetrogeneDB ID: retro_dnov_12

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_92624:5387..5720(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000016722
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSDNOG00000011172
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_dnov_12
GTGACTGTGTATGCTCTGGTGGTGGTGTACTTCCTCATCACTGGAGGAATAATTTATGATGTTATTGTTGAACCTCCAAG
TGTTGGTTCTATGACTGATGAACATGGGCATCAGAGGCCAGTAGCTTTTCTGGCCTACAGAGTAAATGGACAATATATTA
TGGAAGGACTTGCATCCAGCTTCCTGTTTACAGTGGGAGGTTTAGGATTCATAATCTTGGATCGATCCAATGCAGCAAAC
ATTCCAAAACTCAATAGATTTCTTCTCCTATTCAGTTTTTTCATGGCTAGAGTATTGATGAGGATGAAACTACCAGGCTA
TCTGATGGGTTAG

Alignment

ORF - retro_dnov_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFTMGGLG
          .TVYALVVV.YFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFT.GGLG
Retrocopy VTVYALVVV-YFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFTVGGLG

Parental  FIILDRSNAPNIPKLNRFLLLFIGFVCVLL
          FIILDRSNA.NIPKLNRFLLLF..F....L
Retrocopy FIILDRSNAANIPKLNRFLLLFSFFMARVL

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	28.39 RPM
SRP012922_cerebellum	0.00 RPM	6.32 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.27 RPM	12.05 RPM
SRP012922_liver	0.15 RPM	23.07 RPM
SRP012922_lung	0.00 RPM	9.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.11 RPM	14.19 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_12 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 11 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011611	1 retrocopy	retro_btau_753,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Dasypus novemcinctus	ENSDNOG00000011172	2 retrocopies	retro_dnov_12 , retro_dnov_1973,
Homo sapiens	ENSG00000198856	7 retrocopies	retro_hsap_1746, retro_hsap_2013, retro_hsap_2972, retro_hsap_3598, retro_hsap_3686, retro_hsap_376, retro_hsap_4246,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222, retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Myotis lucifugus	ENSMLUG00000000478	2 retrocopies	retro_mluc_1366, retro_mluc_1511,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34,
Tursiops truncatus	ENSTTRG00000003446	1 retrocopy	retro_ttru_582,