RetrogeneDB ID: retro_dnov_2038

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_43755:10697..11644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSB
• Ensembl ID: ENSDNOG00000013450
• Aliases: None
• Description: Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]

Sequence

>retro_dnov_2038
ATGGCTGAAAATGGTGATAATGAAAAAATGGTTGTTCTGGAGGTCAAAATCTGCCATCAAATTGAGTATTATTTTTGGTG
ACTTTAATTTGCCACAGGACTATATTTTAAAAGAACAGATAAAACTTGATGAAGGCTGAGTATCTTTGGAGAAAATGATA
CAATTCAGTAGGTTGATCCATCTAGCAACTGATTTTAATGTAATAGTAGACACATTGAGCAAATCAAAAGAAGAACTCAT
GGAAATAAGTGAAGGTAAAACTTAAATCAGAAGATCTCCAACCATGCCTCTCCCTGAAGTGACCGATGAATTTTAAAATG
ATGTAAAAAATCAGGTTCATTTGTATTAAAGGCTTCTCAACTGGTGCAACCCTTGATGATATAGAGGAATGGTTAGAAGA
TAAAGATCAAGTATAAATACTCACCTGAGAAGAACACTGCACAAAGTATTTAAGGGACAGGTATTTGCTGTGTTTGATAG
CACTGCATCTGTTAATAAATTTGTAGAGACTCCTGGCCAAAAATACAAAGACACAGCCCTGCTAATACTTTCCAAGGAAA
ATTACTTTGCAAAACAGAATGAGGAAGATAGCAAAATAAAGTGGAAGCTAAATTAAGAGCTAAACAAAAGAAAAAATACA
ACAGAAGTTGGAAGAATATGCTGAAATGAAATCTCTAGAAGAAAAGATTGGATGCTTTCTGAAAATCTCAGGTAACATAG
ATGATCAGACTAGTAGAGAGGATATACACATCCTTTTCACAAGTCATAGCAAGATAACATGGATAGACTTTGTCAGAGGA
GCAAAAGAGAGAATAATTCTATTTAAAGAAAAAGCTAAAGAAGCACTGAATAAAGCCAAATATGCAAATAATGTTAACCT
ACAATTAAGGAACAAAGATGTGACATTGGAAGTACTAGAAGGAGAGGTGGAGAAAAGCACTGGAAAA

Alignment

ORF - retro_dnov_2038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.39 %
• Parental protein coverage: 78.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAENGDNEKMAALEAKICHQIEYYF-GDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIV
          MAENGDNEKM..LE.KICHQIEYYF.GDFNLP.D..LKEQIKLDEG.V.LE.MI.F.RL..L.TDFNVIV
Retrocopy MAENGDNEKMVVLEVKICHQIEYYF>GDFNLPQDYILKEQIKLDEG*VSLEKMIQFSRLIHLATDFNVIV

Parental  EALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKN-RSVYIKGFPTDATLDDIKEWLEDKGQV-
          ..LSKSK.ELMEISE.KT.IRRSP..PLPEVTDE..NDVKN.R...IKGF.T.ATLDDI.EWLEDK.QV.
Retrocopy DTLSKSKEELMEISEGKT*IRRSPTMPLPEVTDEF*NDVKN>RFICIKGFSTGATLDDIEEWLEDKDQV<

Parental  LNIQMRRTLHKAFKGSIFAVFDSVDSAKKFVETSGQKYKDTDLLILFKEDYFAKKNEE-RKQNKVEAKLR
          .N...RRTLHK.FKG..FAVFDS..S..KFVET.GQKYKDT.LLIL.KE.YFAK.NEE.R.QNKVEAKLR
Retrocopy INTHLRRTLHKVFKGQVFAVFDSTASVNKFVETPGQKYKDTALLILSKENYFAKQNEE<R*QNKVEAKLR

Parental  AKQEQEE-KQKLAEDAEMRSLEEKVGCLLKFSGDLDDQTCREDLHILFSSHGEIKWIDFVRGAKEGIILF
          AKQ......QKL.E.AEM.SLEEK.GC.LK.SG..DDQT.RED.HILF.SH..I.WIDFVRGAKE.IILF
Retrocopy AKQKKKY<QQKLEEYAEMKSLEEKIGCFLKISGNIDDQTSREDIHILFTSHSKITWIDFVRGAKERIILF

Parental  KEKAKEALDKAKDANNGNLQLRNKDVTWEVLEGEVEKEALK
          KEKAKEAL.KAK.ANN.NLQLRNKDVT.EVLEGEVEK...K
Retrocopy KEKAKEALNKAKYANNVNLQLRNKDVTLEVLEGEVEKSTGK

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	93.93 RPM
SRP012922_cerebellum	0.00 RPM	141.87 RPM
SRP012922_heart	0.00 RPM	67.99 RPM
SRP012922_kidney	0.00 RPM	107.33 RPM
SRP012922_liver	0.00 RPM	52.48 RPM
SRP012922_lung	0.00 RPM	119.74 RPM
SRP012922_quadricep_muscle	0.00 RPM	53.48 RPM
SRP012922_spleen	0.00 RPM	138.73 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_2038 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038 ,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000011507	3 retrocopies	retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,