RetrogeneDB ID: retro_dnov_1315

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18075:59374..60027(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSDNOG00000013799
• Aliases: None
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_dnov_1315
GGACCATCAACTGATAAAGACTCTGAAGAAAAGAAAAAGAACCTGCAATGACATCATAGAATAACCCTGAAGCAAGAGAA
GAAAGGAGCTCCAGTGGCAATGTAAGCAGCAGAAAGGTCGAGAAAGATGCTGGAGATGCTTAGGTTTGGTCTTTTCCTCG
GGCACCAAGCACTTCTGACTCTGTACGGTTAAAGTGTTGGGAGATGCTTGCTGTAGCTCTCTGAACAGGAGATGACTACA
TTGCTATTGGAGCTGATGAGGAAGAATTAGGATCTCAAATTGAGGAAGCTATATATCAAGAAATAAGGAATACAGACATG
AAATCTAAAGTACGAAGTAGGATATCAAACCTTAAGGATGCAAAGAATCCAAACTTAAGGAAAAATGTACTGTGTGGGAA
TATTCCTCCTGAGTTATTTGCTAGAATGACAGCAGAGGAAATGACTAGTGATGAGTTCAAAGAGATGAGGAAAAACTTGA
CCAAAGAAGCCATCAGAGAGCATCAAATGGCCAAAACAGGTGGAACCCAGACTGACTTCTTCACATGTGGCAAATGTAAA
AAGAACTGTACTTACATGCAGGTTCAAACACATAGTACTGATGAACTGATGACAACATTTGTCATCTGTAATGAATGTGG
AAATCGATGGAAG

Alignment

ORF - retro_dnov_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPSTDKDS-EKKK-EPTMTSQNSPEAREESSSSGNVSSRKDETNARDTYVSSFPRAPSTSDSVRLKCREM
          GPSTDKDS.EKKK.EP.MTS.N.PEAREE.SSSGNVSSRK.E..A.D..V.SFPRAPSTSDSVRLKC.EM
Retrocopy GPSTDKDSEEKKK<EPAMTS*NNPEAREERSSSGNVSSRKVEKDAGDA*VWSFPRAPSTSDSVRLKCWEM

Parental  LAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPP
          LA.AL.TGDDYIAIGADEEELGSQIEEAIYQEIRNTDMK.K..VRSRISNLKDAKNPNLRKNVLCGNIPP
Retrocopy LAVAL*TGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKSK--VRSRISNLKDAKNPNLRKNVLCGNIPP

Parental  DLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDFFTCGKCKKKNCTYTQVQTRSADEPMTT
          .LFARMTAEEM.SDE.KEMRKNLTKEAIREHQMAKTGGTQTDFFTCGKCKK.NCTY.QVQT.S.DE.MTT
Retrocopy ELFARMTAEEMTSDEFKEMRKNLTKEAIREHQMAKTGGTQTDFFTCGKCKK-NCTYMQVQTHSTDELMTT

Parental  FVVCNECGNRWK
          FV.CNECGNRWK
Retrocopy FVICNECGNRWK

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	5.25 RPM	22.17 RPM
SRP012922_cerebellum	2.61 RPM	14.98 RPM
SRP012922_heart	0.93 RPM	7.89 RPM
SRP012922_kidney	4.11 RPM	17.25 RPM
SRP012922_liver	2.17 RPM	12.69 RPM
SRP012922_lung	6.57 RPM	29.02 RPM
SRP012922_quadricep_muscle	0.87 RPM	5.54 RPM
SRP012922_spleen	7.55 RPM	32.96 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_1315 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315 , retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,