RetrogeneDB ID: retro_dnov_696

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_930:56209..56854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMXL1
• Ensembl ID: ENSDNOG00000017199
• Aliases: None
• Description: RNA binding motif protein, X-linked-like 1 [Source:HGNC Symbol;Acc:25073]

Sequence

>retro_dnov_696
ATGGCTGAAGCAGATCATCCAGGAAAGCTTTTCATTGGTGGGTTCAATACAGAAACAAATGAAAAAGTCCTTGAAGCAGT
ATTTAGCAAATATGGACGAATAGTGGAACTACTCATGATGAAAGACCATGAAACCAACAAATCAAGAGGTTTCGCTTTTG
TCACCTTTGAAAATCCAGCAGATGCCAAGGATGCAGTCAGAGACATGAATGGAAAGTCCTTAGATGGAAAAGCCATTGAG
GTGGAACAAGCCATTAAACCATCATTTGAAAGTGGCAGACATGGACCACCTCCAAGAAGCAGAGGCCTCCCTAGAGGTCC
TAGAGGTGGAAGAGGAGGAAGTGGAGGAACCAGGAGACCTCCCTCACATGCAGGGCACATGGACGATGGAGGCTATTCCA
TGAATTTTAACATGAGTTCTTCCAGGGAACCACTTCAAGTAAAAAGAGGACCACCATCACAACGTGGGGGTCCTCCTCTT
AAAAGATCTACCCCCTCAGGGTCAGTTCACAGCAGCAGTGGAATGGGAGGGAGAGCTCCTTTATCACATGGAAGAGAGGG
TTATGGAGGCCCAACACGAAGGGAACCCCTGTCCTCTTGGAGAGATATTTATTTATCCCCAAGAGATGATGGACATTCTA
CTAAA

Alignment

ORF - retro_dnov_696 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.96 %
• Parental protein coverage: 55.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
          M.EAD.PGKLFIGG.NTETNEK.LEAVF.KYGRIVE.L.MKD.ETNKSRGFAFVTFE.PADAKDA.RDMN
Retrocopy MAEADHPGKLFIGGFNTETNEKVLEAVFSKYGRIVELLMMKDHETNKSRGFAFVTFENPADAKDAVRDMN

Parental  GKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMDFNM
          GKSLDGKAI.VEQA.KPSFESGR.GPPP..RSRG.PRG...........R.PPS..GHMDDGGYSM.FNM
Retrocopy GKSLDGKAIEVEQAIKPSFESGRHGPPP--RSRGLPRGPXXXXXXXXXXRRPPSHAGHMDDGGYSMNFNM

Parental  TSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPR
          .SSR.PL.VKRGPP...GGPP.KRS.PSG.V.SSSGMGGRAP.S.GR..YGGP.RREPL.S.RD.YLSPR
Retrocopy SSSREPLQVKRGPPSQRGGPPLKRSTPSGSVHSSSGMGGRAPLSHGREGYGGPTRREPLSSWRDIYLSPR

Parental  DDGYSTK
          DDG.STK
Retrocopy DDGHSTK

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	83.23 RPM
SRP012922_cerebellum	0.00 RPM	71.07 RPM
SRP012922_heart	0.00 RPM	33.88 RPM
SRP012922_kidney	0.00 RPM	49.83 RPM
SRP012922_liver	0.00 RPM	31.43 RPM
SRP012922_lung	0.31 RPM	79.87 RPM
SRP012922_quadricep_muscle	0.00 RPM	36.35 RPM
SRP012922_spleen	0.11 RPM	106.79 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_696 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 17 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696 ,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica	ENSMODG00000014054	1 retrocopy	retro_mdom_1231,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,