RetrogeneDB ID: retro_dnov_2648

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_94081:5315..5667(+)
• 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_2648
CGTGTCGGGCGCACCCACGAGATCAGCTCAAGCCCCCGCAGGGCCTCGTGCCCTCCACCTCCGTGCACTTGGAGGACCCC
CGAGGTGCCGAGGGGACCGTGTATGGAAGGGGGGCTATGATTACAGCCAGGGTCGGCTTCGTGGGGAGTTTCCCAGGACA
CAGGGAGGTGGGGTGCATGGCCTGTGGGGGGGAATGGGCCTCCCACAAGAGGATCTGGTTCCAAGTTCTTGTTGCAGGAC
TTCCTCCTTGAGGCAGCTGGCAGGACCTCCACCTGCGGGAGACTGGGGATGCCTGTTACGCAGATGTGCAGGAGGATGGA
ATCGGATGGTTGAATAGCTCAGGAAAGAAGAG

Alignment

ORF - retro_dnov_2648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 55.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KYGRIREI-ELKNRHGLVPFAFVRFEDPRDAEDAIYGRN-GYDYGQCRLRVEFPRTYGGR-GGWPRGGRN
          ..GR..EI..LK...GLVP...V..EDPR.AE...YGR..GYDY.Q.RLR.EFPRT.GG..G.WP.GG.N
Retrocopy RVGRTHEI<QLKPPQGLVPSTSVHLEDPRGAEGTVYGRG<GYDYSQGRLRGEFPRTQGGG<GAWPVGG-N

Parental  GPPTRRSD-FRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMG-MVEYLRKED
          GPPTR.S..F.VLV.GLPP.GSWQDL..H.RE.GD.CYADVQ.DG.G.MVE.LRKE.
Retrocopy GPPTRGSG<FQVLVAGLPP*GSWQDL--HLRETGDACYADVQEDGIG<MVE*LRKEE

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_2648 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,