RetrogeneDB ID: retro_dnov_1985

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_40391:12869..13195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSDNOG00000010243
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_dnov_1985
GTAACTCTCTGGATGAGGAAGTTCATGACCAACAGGCCACGTCAGCAGGAAAGAATGGTCATCAGTGTCCTTCACCCTGG
GAAGGCAACAGAAGACAGAAATCCAGGAAAAACCAGCCCAATGTACAAGACCACACCGGACATCATCTCTGTGTTTGGAT
TCAGAACTCATCTTGGTGGTGGCAAGACAACAGGCATTGCCATGATGTAGGATTCCTTGGATTATGCAAAGAAAATGAGC
CCAAACACAGACTTGCAAGGCTCGGCCTGTATGAGAACACAAGGACCTCAAGAAAACAGCAGATGGAACGCAAGAGTAGA
ACGAAG

Alignment

ORF - retro_dnov_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 84.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGM
          VT...RKFMTNR..Q...MVI.VLHPGKAT........K...MYKTTPD.I.VFGFRTH.GGGKTTG..M
Retrocopy VTLWMRKFMTNRPRQQERMVISVLHPGKATEDRNP--GKTSPMYKTTPDIISVFGFRTHLGGGKTTGIAM

Parental  IYDSLDYAKK-NEPKHRLARHGLYEKKKTSRKQRKERKNRMK
          ..DSLDYAKK.NEPKHRLAR.GLYE...TSRKQ..ERK.R.K
Retrocopy M*DSLDYAKK<NEPKHRLARLGLYENTRTSRKQQMERKSRTK

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	508.73 RPM
SRP012922_cerebellum	0.00 RPM	443.89 RPM
SRP012922_heart	0.00 RPM	344.57 RPM
SRP012922_kidney	0.00 RPM	493.11 RPM
SRP012922_liver	0.00 RPM	210.38 RPM
SRP012922_lung	0.00 RPM	749.27 RPM
SRP012922_quadricep_muscle	0.00 RPM	541.93 RPM
SRP012922_spleen	0.00 RPM	970.06 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_1985 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 7 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010243	18 retrocopies	retro_dnov_1299, retro_dnov_1305, retro_dnov_1394, retro_dnov_1444, retro_dnov_1470, retro_dnov_1471, retro_dnov_168, retro_dnov_1889, retro_dnov_1920, retro_dnov_1985 , retro_dnov_2074, retro_dnov_2357, retro_dnov_288, retro_dnov_309, retro_dnov_551, retro_dnov_73, retro_dnov_782, retro_dnov_92,
Echinops telfairi	ENSETEG00000007481	32 retrocopies	retro_etel_1119, retro_etel_1242, retro_etel_1274, retro_etel_1339, retro_etel_1395, retro_etel_1663, retro_etel_1688, retro_etel_1783, retro_etel_1800, retro_etel_1806, retro_etel_183, retro_etel_1901, retro_etel_1934, retro_etel_1978, retro_etel_1991, retro_etel_2040, retro_etel_2104, retro_etel_223, retro_etel_287, retro_etel_289, retro_etel_369, retro_etel_422, retro_etel_476, retro_etel_503, retro_etel_523, retro_etel_67, retro_etel_744, retro_etel_752, retro_etel_815, retro_etel_904, retro_etel_91, retro_etel_94,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,