RetrogeneDB ID: retro_dnov_380

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4245:342964..343450(+)
• Located in intron of: ENSDNOG00000017318

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSDNOG00000005917
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_dnov_380
TTACGGAGGCATTTCTTAAGTGATGGAGATGGTGCTGGTGTTGAACCGAGAATTCATCTTCTAGTGCAGAGTTTCATTAA
ATGGTGCAGCTCTGGATCCCAGGAAGAGGGATGTGTCCAGTACCAACATATGCTGAGCGCCCTATCACAGTGAGACTTTT
CACTGGGCAAAACCTTATTGTTATAGATGAACCTCAGAAAAATGGAAAATTATGAAAAAATTGACAAAGAAATAGAATGT
AGCATTACCGGAACACATGAAAAAATTGCTGATGGCAAAAAGCAAATTTTTCAAACAAAATGAATATGAAAAAAACATCA
AGAATATGATGCTTTGGCAAAAGTGATCCAGCATCATCCAGACAGGCATGAGACATTAAAGGAACTAGAGGCTCTGGAAA
AAGAACTAGAGCATCTTTCATCTAGTAAAGAAAGCATTGAAGATAAGCTGCATTTGAGACTGAAACAGATTCACGTGCTC
TTAGCA

Alignment

ORF - retro_dnov_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.85 %
• Parental protein coverage: 79.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLREME
          .R...L.DGDGAG...RI.LLV.SFIKWC.SGSQEEG..QYQ.MLS.LSQ..FS.GKTLL...MNLR.ME
Retrocopy LRRHFLSDGDGAGVEPRIHLLVQSFIKWCSSGSQEEGCVQYQHMLSALSQ*DFSLGKTLLL*-MNLRKME

Parental  NYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELEALGKELEHL
          NYEKI.KEIECSI.G.HEKIA..KKQI.Q.K.I.K..QEYDALAKVIQHHPDRHETLKELEAL.KELEHL
Retrocopy NYEKIDKEIECSITGTHEKIADGKKQIFQTK*I*KKHQEYDALAKVIQHHPDRHETLKELEALEKELEHL

Parental  SHIKESVEDKLELRRKQFHVLLS
          S..KES.EDKL.LR.KQ.HVLL.
Retrocopy SSSKESIEDKLHLRLKQIHVLLA

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	0.00 RPM	40.06 RPM
SRP012922_cerebellum	0.00 RPM	39.32 RPM
SRP012922_heart	0.00 RPM	16.47 RPM
SRP012922_kidney	0.00 RPM	29.30 RPM
SRP012922_liver	0.00 RPM	16.72 RPM
SRP012922_lung	0.00 RPM	49.02 RPM
SRP012922_quadricep_muscle	0.00 RPM	21.46 RPM
SRP012922_spleen	0.00 RPM	32.16 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_380 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 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380 ,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,