RetrogeneDB ID: retro_dnov_2464

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_77337:6115..6979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIP13
• Ensembl ID: ENSDNOG00000015202
• Aliases: None
• Description: thyroid hormone receptor interactor 13 [Source:HGNC Symbol;Acc:12307]

Sequence

>retro_dnov_2464
GTGTTTGGTGATTACACATAGACTTGAGTTTGATGATCATTTTCTGGCCAGAAATGTGCAATCTGTGTCTATCGTTGACA
CAGAGTTAAAAGCTAAAGAACCACAGCCCATTGATTTGAGCACATGTACTCTCGCACTTAACATCTTCCAACTCAACGAG
GATGGCCCCAGCAGTGAAAACTTGGAGGAAGAGACAGAAAATGTCATTGCAGCAAATCACTGGGTTCTGCCGGCGGCTGG
ATTCCATGGTCTCTGGGACAGCCTGGTATATGACGTGGAGGTTAAATCACACCTCCTCGATTACGTGACGGCAACCTTAC
TGTTTTCAGACAGAAACGTTGACAGCAACTTGATAACCTGGAACCGAGTTCTGTTGCTGCACGGTCCTCCAGGAACTGGA
AAAACATCCCTGTGTAAAGCATTGGCCCAGAAACTGACCATTAGACTGTCAAGCAGGTACCGATTTGGCCAGTTAATTGA
AATAAACAGTCACGGCCTCTTTTCCAAGTGGTTTTCCGAAAGCGGCAAGCTGGTGACTAAGATGTTCCAGAAGATCCAGG
ACTCGACTGACGACGAAGATGCTCTGGTGTTTGTGCTGATCGACGGGGCGGAAAGGCTCACGGCAGCCCGCAACGCCTGC
GGGGCCGGCACGGAGCCCTCGGACGCCATCCGCGTGGTCAGTGCCGTCCTGACCCAGATCGACCAGGTTAAAAGGCACTC
GAACGTGGTGATACTCGCCACGTCCAACATCACCGAGAGGATCGACGCGGCCTTCGTGGACAGAGCCGACATCAGGCAGC
AATAGGCGCCCCCTCGGCGGCAGCCATCTTCAAAATCTCGCTCCTGTCGGAAGAACTAATGAAG

Alignment

ORF - retro_dnov_2464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 66.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFGDYTWT-EFDDHFLARNVQSVSIVDTELKVKDPQPIDLSTCSLALHIFQLNEDGPSSENLEEETENII
          VFGDYT.T.EFDDHFLARNVQSVSIVDTELK.K.PQPIDLSTC.LAL.IFQLNEDGPSSENLEEETEN.I
Retrocopy VFGDYT*T>EFDDHFLARNVQSVSIVDTELKAKEPQPIDLSTCTLALNIFQLNEDGPSSENLEEETENVI

Parental  AANHWVLPAADFHGLWDSLVYDVEVKSHLLDYVTTTLLFSDRNVDSNLISWNRVVLLHGPPGTGKTSLCK
          AANHWVLPAA.FHGLWDSLVYDVEVKSHLLDYVT.TLLFSDRNVDSNLI.WNRV.LLHGPPGTGKTSLCK
Retrocopy AANHWVLPAAGFHGLWDSLVYDVEVKSHLLDYVTATLLFSDRNVDSNLITWNRVLLLHGPPGTGKTSLCK

Parental  ALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDSIEDKDALVFVLIDEVESLTAA
          ALAQKLTIRLSSRYR.GQLIEINSH.LFSKWFSESGKLVTKMFQKIQDS..D.DALVFVLID..E.LTAA
Retrocopy ALAQKLTIRLSSRYRFGQLIEINSHGLFSKWFSESGKLVTKMFQKIQDSTDDEDALVFVLIDGAERLTAA

Parental  RNACRAGTEPSDAIRVVNAVLTQIDQVKRHSNVVILTTSNITERIDVAFVDRADIKQY-IGPPSAAAIFK
          RNAC.AGTEPSDAIRVV.AVLTQIDQVKRHSNVVIL.TSNITERID.AFVDRADI.Q..IG.PSAAAIFK
Retrocopy RNACGAGTEPSDAIRVVSAVLTQIDQVKRHSNVVILATSNITERIDAAFVDRADIRQQ<IGAPSAAAIFK

Parental  IYLSCLEELMK
          I.L...EELMK
Retrocopy ISL-LSEELMK

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	1.56 RPM	12.83 RPM
SRP012922_cerebellum	2.06 RPM	1.79 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.55 RPM	1.64 RPM
SRP012922_liver	0.62 RPM	2.01 RPM
SRP012922_lung	2.14 RPM	8.71 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.25 RPM
SRP012922_spleen	2.40 RPM	20.49 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_2464 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007439	1 retrocopy	retro_chof_2003,
Callithrix jacchus	ENSCJAG00000003849	1 retrocopy	retro_cjac_1987,
Dasypus novemcinctus	ENSDNOG00000015202	1 retrocopy	retro_dnov_2464 ,
Oryctolagus cuniculus	ENSOCUG00000006144	1 retrocopy	retro_ocun_155,
Pongo abelii	ENSPPYG00000015309	1 retrocopy	retro_pabe_1358,