RetrogeneDB ID: retro_dnov_1702

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_27052:41443..41720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSDNOG00000000421
• Aliases: None
• Description: serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]

Sequence

>retro_dnov_1702
ATGCATCATAATTCCTGTCCATTGCACTATAAGGTTTATGTAGGTAATCTTGAAAACAATGGCAACAAGACTGAATTGGG
ACAGGCTTTTGGATATTATGGACCACTCTGAAGGTGTGTGGGTACCTAGAAACCCTCCTGACTTTGCTTTTATTGAATTT
GAAGATGCCGGAGATGCAGCTAATGCTGAGAATTAGATGAAAGAACACTCTATGGCTGCTGTGTAAGAATGGAACCGTCC
AATGGTGAAAAAAAGAAGTCATAATTGAGGCCCTCCT

Alignment

ORF - retro_dnov_1702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.11 %
• Parental protein coverage: 56.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPL-RSVWVARNLPGFAFVXXXXXXXAADAVREL-DK
          MH..SCPL..KVYVGNL.NNGNKTEL..AFGYYGPL...VWV.RN.P.FAF........AA.A.......
Retrocopy MHHNSCPLHYKVYVGNLENNGNKTELGQAFGYYGPL>EGVWVPRNPPDFAFIEFEDAGDAANAEN*M<ER

Parental  TLCGCRVRVELSNGE-KRSRNRGPP
          TL.GC.VR.E.SNGE.KRS.N.GPP
Retrocopy TLYGCCVRMEPSNGE>KRSHN*GPP

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	82.84 RPM
SRP012922_cerebellum	0.00 RPM	33.68 RPM
SRP012922_heart	0.00 RPM	20.65 RPM
SRP012922_kidney	0.00 RPM	19.44 RPM
SRP012922_liver	0.00 RPM	28.79 RPM
SRP012922_lung	0.00 RPM	58.49 RPM
SRP012922_quadricep_muscle	0.00 RPM	11.08 RPM
SRP012922_spleen	0.00 RPM	74.40 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_1702 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 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
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,
Equus caballus	ENSECAG00000018741	2 retrocopies	retro_ecab_178, retro_ecab_961,
Gorilla gorilla	ENSGGOG00000017186	5 retrocopies	retro_ggor_1654, retro_ggor_1706, retro_ggor_2030, retro_ggor_2746, retro_ggor_630,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Oryctolagus cuniculus	ENSOCUG00000006684	3 retrocopies	retro_ocun_415, retro_ocun_772, retro_ocun_970,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Pan troglodytes	ENSPTRG00000018106	4 retrocopies	retro_ptro_1566, retro_ptro_1628, retro_ptro_2776, retro_ptro_533,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,