RetrogeneDB ID: retro_dnov_1555

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_234088:763..1283(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSDNOG00000012598
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_dnov_1555
GAGGACTTGTTCTACAAGTATGGCCACATCCAGGAGATCAAGCTCAAGAACCAACATGGCCTCATGCCCTTTGTGCACTT
TGAGGACCCCGAGATGCTGAGGATGCAATTTTTGGAAGGAATGGTTTGATTAAGGTCAGTGTAGGCTTCGTGTAGAGTAA
CCCAGGTCTTATGGTGGTTGGGGTGGATGGCCCTGTGGTGGGAGGAATGGGCCTCCCACAAGAAGATCTGATTTCTGAGT
TCTTCTTTCAGGACTTCTTCCATCAGCAGCTGGCAGGACCTGAAGGATCACATGCAAGAGGCTGGGGATGTCTGTTATGC
AGATGTGCAGAAGGATGGAATGGGTATGGTTGAATATCTGAGAAAATAAGACGTGGAATATGTCCTGCTTAAACTGGATG
ACACCAAATTCCACTCTCATGAGGGTGAAACTTCTTCCATTAGAGTTTATCCAGAGAGAAGCACCAGCTATGGCTACTCT
TGCTCTCGACTGCCCATATCAAAGCAGGGGTTCACCATAC

Alignment

ORF - retro_dnov_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 79.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EDLFYKYGRIREIELKNRHGLVPFAFVRFEDP-RDAEDAIYGRNG-YDYGQCRLRVEFPRTYGGRGGWPR
          EDLFYKYG.I.EI.LKN.HGL.PF..V.FEDP.RDAEDAI.GRNG..D.GQCRLRVE.PR.YGG.GGWP.
Retrocopy EDLFYKYGHIQEIKLKNQHGLMPF--VHFEDP<RDAEDAIFGRNG<FD*GQCRLRVE*PRSYGGWGGWPC

Parental  GGRNGPPTRRSDFRVLVSGLPPSG-SWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDD
          GGRNGPPTRRSDF.VL.SGL.PS..SWQDLKDHM.EAGDVCYADVQKDGMGMVEYLRK.D.EY.L.KLDD
Retrocopy GGRNGPPTRRSDF*VLLSGLLPSA<SWQDLKDHMQEAGDVCYADVQKDGMGMVEYLRK*DVEYVLLKLDD

Parental  TKFRSHEGETSYIRVYPERSTSYGYSRSR-SGSRGRDSPY
          TKF.SHEGETS.IRVYPERSTSYGYS.SR......R.SPY
Retrocopy TKFHSHEGETSSIRVYPERSTSYGYSCSR>CPYQSRGSPY

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	69.81 RPM
SRP012922_cerebellum	0.00 RPM	40.97 RPM
SRP012922_heart	0.00 RPM	7.43 RPM
SRP012922_kidney	0.00 RPM	58.32 RPM
SRP012922_liver	0.00 RPM	39.63 RPM
SRP012922_lung	0.00 RPM	49.02 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.50 RPM
SRP012922_spleen	0.00 RPM	48.30 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_1555 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000000421	9 retrocopies	retro_dnov_1326, retro_dnov_1513, retro_dnov_1702, retro_dnov_1951, retro_dnov_2153, retro_dnov_2328, retro_dnov_2491, retro_dnov_569, retro_dnov_784,
Dasypus novemcinctus	ENSDNOG00000007821	2 retrocopies	retro_dnov_317, retro_dnov_829,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555 , retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,