RetrogeneDB ID: retro_dnov_2389

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_70032:4997..5373(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSDNOG00000017960
• Aliases: None
• Description: STARD3 N-terminal like [Source:HGNC Symbol;Acc:19169]

Sequence

>retro_dnov_2389
CTGTTTGTCACCTTTGACCTCTTATTTGTAACATTACTGCAGATAATAGAGGTAAATGTGAATGGAGGTATTGAGAATAC
GTTAGAGAAGGTAGTACATGATAACTACTGCTCTTCTTATTTTGATATATTTATTTTCACAGTGTTTCAATTTAAAATAT
TAATACATGCATATGCTGTATGCAAACTGAGCCATTGGTGGGCAATTGTGCTGATGACAGCAGTGATCACGGCTTTCTTA
TTAGCAAAAACAGTCCTTTCGAAGCTTTTCTCTCAAGGGGCTTTTGGCTATGTGCTGCCCATCATTTCATTCCATCCTTA
CCTGGATTGAGACCTGGTTCCTGGATTTCAAAGTGTTACCTCAAGAAGCAGAGGAA

Alignment

ORF - retro_dnov_2389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFVTFDLLFVTLLWIIELNVNGGIENTLEKEVVHYDYYSSYFDIFLLAVFRFKVLILAYAVCKLRHWWAI
          LFVTFDLLFVTLL.IIE.NVNGGIENTLEK.VVH..Y.SSYFDIF...VF.FK.LI.AYAVCKL.HWWAI
Retrocopy LFVTFDLLFVTLLQIIEVNVNGGIENTLEK-VVHDNYCSSYFDIFIFTVFQFKILIHAYAVCKLSHWWAI

Parental  ALTTAVTSAFLLAKVILSKLFSQGAFGYVLPIISF-ILAWIETWFLDFKVLPQEAEE
          .L.TAV..AFLLAK..LSKLFSQGAFGYVLPIISF.IL.WIETWFLDFKVLPQEAEE
Retrocopy VLMTAVITAFLLAKTVLSKLFSQGAFGYVLPIISF>ILTWIETWFLDFKVLPQEAEE

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	10.89 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	3.48 RPM
SRP012922_kidney	0.27 RPM	12.59 RPM
SRP012922_liver	0.15 RPM	4.80 RPM
SRP012922_lung	0.15 RPM	10.69 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.11 RPM	18.89 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_2389 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389 ,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,