RetrogeneDB ID: retro_dnov_32

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_28689:17795..18617(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000008776
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSDNOG00000006719
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta [Source:HGNC Symbol;Acc:130]

Sequence

>retro_dnov_32
GTGCTGCTGACTGAGGCGCCCCTGAACCCCAAGGCCAACCGTGAGAAGATGACGCAGATCATGTTCGAGACCTTCAACAC
GCCGGCCATGTACGTGGCCATCCAGGCCGTGCTGTCGCTGTACGCCTCCGGCCGCACCACGGGCATCGTCATGGACTCCG
GCGACGGCGTCACCCACACCGTGCCCATCTACGAGGGCTACGCGCTGCCCCACGCCATCCTGCGTCTGGACCTGGCTGGC
CGCGACCTGACCGACTACCTCATGAAGATCCTCACGGAGCGCGGCTACAGCTTCACCACCACGGCCGAGCGCGAGATCGT
GCGCGACATCAAGGAGAAGCTGTGCTACGTCGCCCTGGACTTCGAGCAGGAGATGGCCACCGCCGCGTCCTCCTCCTCCC
TGGAGAAGAGCTACGAGCTGCCCGACGGGCAGGTCATCACCATCGGCAACGAGCGGTTCCGCTGCCCCGAGGCCCTCTTC
CAGCCCTCCTTCCTGGGCATGGATTCCTGTGGCATCCACGAAACTACCTTCAACTCCATCATGAAGTGTGACGAGGAGAT
CTACAAAGACCTCTACACCAGCATGGTGCTGTCCGGTGGAACCACCATGTACCCCGGCATCGCCGACAGGATGCAGAAGG
AGATCACGGCGCTGGCTCCCAGCACGATGAAGATCAAGATCATCGCCCCCCCTGAGCGCAAGTACTCGGTGTGGATCGGC
GGCTCCATCCTGGCCTCGCTGTCCACCTTCCAGCAAATGTGGATCAGCAAGCAGGAGTACGACGAGTCCGGCCCCTCCAT
CGTCCACCGCAAATGCTTCTAG

Alignment

ORF - retro_dnov_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.38 %
• Parental protein coverage: 72.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPH
          LLTEAPLNPKANREKMTQIMFETFN.PAMYVAIQAVLSLYASGRTTGIV.DSGDGVTH.VPIYEGYALPH
Retrocopy LLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPH

Parental  AIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELP
          AI.RLDLAGRDLTDYLMKILTERGYSF.TTAEREIVRDIKEKLCYVALDFE.EMATAASSSSLEKSYELP
Retrocopy AILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELP

Parental  DGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRM
          DGQVITIGNERFRCPE.LFQPSF.GM.S.GIHETT.NSIMKCD..I.KDLY...VLSGGTTMYPGIADRM
Retrocopy DGQVITIGNERFRCPEALFQPSFLGMDSCGIHETTFNSIMKCDEEIYKDLYTSMVLSGGTTMYPGIADRM

Parental  QKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDEAGPSIVHRKCF
          QKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDE.GPSIVHRKCF
Retrocopy QKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

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	1955.76 RPM	520.20 RPM
SRP012922_cerebellum	745.77 RPM	7.01 RPM
SRP012922_heart	568.01 RPM	34.11 RPM
SRP012922_kidney	594.14 RPM	124.85 RPM
SRP012922_liver	625.57 RPM	30.50 RPM
SRP012922_lung	1642.09 RPM	418.77 RPM
SRP012922_quadricep_muscle	2540.36 RPM	101.08 RPM
SRP012922_spleen	1903.72 RPM	1536.07 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_32 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32 ,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,