RetrogeneDB ID: retro_dnov_317

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3548:95123..95502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF7
• Ensembl ID: ENSDNOG00000007821
• Aliases: None
• Description: serine/arginine-rich splicing factor 7 [Source:HGNC Symbol;Acc:10789]

Sequence

>retro_dnov_317
CCACCTGCCTGATGTCCCTTTGATGCTAATGATAGATGCTATGAGTGTAGTGAAAGGGACATTATGCTTATGATTGTCAT
CGCTAGAGCCGGCTGTGAAGGAGCTGGCCATGGTCTAGAGTGCATTCGAGATCCAGAGGAGGGCCATACTGTCACAGGAG
CAGAGGATGCAGGGCAAGATCAGCATCAACTCAACTATCAAGATCTGTGTCTCCTCGTAGATCGAGTTCTGCTTCACTCA
GAAGCTCTGGGCCTGGTTCTATAAAAGCATCGGGATATTTCCAATCCCGGTCAAAGTCTAGGTCAAGATCCAGTCTATTT
CACGAACAAGGAGCAGCCCATCAAAATCCAGATCACCATCTCCCAGAAGGAAGTCCACG

Alignment

ORF - retro_dnov_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.73 %
• Parental protein coverage: 57.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPARRPFDPNDRCYECGE-KGHYAYDCHRYSRRRRSSSRSRSHSRSRRRRYSRSRSRSRGRRSRSVSLRR
          PPA..PFD.NDRCYEC.E.KGHYAYDCHR.SR..RS...SR.HSRSR...Y.....RSRG.R.RS.S...
Retrocopy PPA*CPFDANDRCYECSE<KGHYAYDCHR*SRL*RSWPWSRVHSRSRGGPYCH---RSRGCRARSASTQL

Parental  SRSASLRRSRSGSIKGSRYFQSRSRSRSRSRSISRPRSSRSKSRS-PSPKRSRSPSGSPRRSAS
          SRS.S.RRS.S.S...S............SRS.SR.RSS........SP..SRSP..SPRR...
Retrocopy SRSVSPRRSSSASLRSSGPGSIKASGYFQSRSKSRSRSSLFHEQG<SSPSKSRSP--SPRRKST

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	0.19 RPM	90.43 RPM
SRP012922_cerebellum	0.00 RPM	65.99 RPM
SRP012922_heart	0.00 RPM	19.49 RPM
SRP012922_kidney	0.00 RPM	50.38 RPM
SRP012922_liver	0.00 RPM	63.63 RPM
SRP012922_lung	0.15 RPM	124.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	14.37 RPM
SRP012922_spleen	0.11 RPM	130.83 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_317 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 12 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015988	1 retrocopy	retro_amel_1025,
Canis familiaris	ENSCAFG00000029620	1 retrocopy	retro_cfam_652,
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,
Macropus eugenii	ENSMEUG00000016459	1 retrocopy	retro_meug_1048,
Myotis lucifugus	ENSMLUG00000009536	2 retrocopies	retro_mluc_2005, retro_mluc_972,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289,
Mus musculus	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
Rattus norvegicus	ENSRNOG00000027360	11 retrocopies	retro_rnor_1535, retro_rnor_1977, retro_rnor_1984, retro_rnor_2419, retro_rnor_2420, retro_rnor_2421, retro_rnor_2495, retro_rnor_2501, retro_rnor_2502, retro_rnor_2503, retro_rnor_478,
Sarcophilus harrisii	ENSSHAG00000015970	1 retrocopy	retro_shar_72,