RetrogeneDB ID: retro_dnov_1672

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_262082:44..671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP1
• Ensembl ID: ENSDNOG00000008688
• Aliases: None
• Description: poly(rC) binding protein 1 [Source:HGNC Symbol;Acc:8647]

Sequence

>retro_dnov_1672
ATGGACACCAGTGTGATTGAAGGTGGATTAAATGTCACTCTCACCATTTGGCTACTTATGCATGGAAAGGAAGTTGGCAG
TATCATCGGAAAGAAAGGAGAATCAGTTAAGATGCGGGAGGAAAGTGATGGGCACATCAACATCTAAGAAGGTAATTGTC
CTGAGAGAATTATCACTTGGGCTGGGCTCACTAATGCCACCTTTAAAGCCTTTGTTATGATCATTGGCAAACTGGAAGAG
GACTACAGCAGCTCTATGACTAATAGCACAGCTGCCAGTAGACCCCCAGTCACCCTGAGGCTGCTGGTCCATGCTAGTCA
ATGTGGCTCTCTCATTGGGAAAGGTGGTTGCAAGATCAAGGAAATACGAGAGTACAGCGGCTCAGGGCCAGGTGGCAGGG
GATATGCACCCCAACTCAACTGAGCGGGCCATCACTATCGCTGGCATTCCTCAGTCCATCACTGAGTGTGTCAAACAGAT
CTGCGTGGTCATGTTGGAGTCCCCCCCAAGGGTTTGATCATCCCGTACCGGCCCAAGCCCTCCAGTTCTCCGGTCATCTT
TGCAGGTAATCAGGACAGATGCAGCACAGGCAGCGACGGTGTGAGCTTTCCCCACACTACCACTGTG

Alignment

ORF - retro_dnov_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.18 %
• Parental protein coverage: 59.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MDT.VIEGGLNVTLTI.LLMHGKEVGSIIGKKGESVK.MREES...INI.EGNCPERIIT.AG.TNA.FK
Retrocopy MDTSVIEGGLNVTLTIWLLMHGKEVGSIIGKKGESVK-MREESDGHINI*EGNCPERIITWAGLTNATFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSL-IGKGGCKIKEIRESTGAQVQVAGDMLP
          AF.MII.KLEED.SSSMTNSTAASRPPVTLRL.V.ASQCGSL..GK.........EST.AQ.QVAGDM.P
Retrocopy AFVMIIGKLEEDYSSSMTNSTAASRPPVTLRLLVHASQCGSL>LGKVVARSRKY-ESTAAQGQVAGDMHP

Parental  NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP-KGVTIPYRPKPSSSPVIFAGGQDRYSTGSDSAS
          NSTERAITIAGIPQSI.ECVKQICVVMLE....SPP.KG..IPYRPKPSSSPVIFAG.QDR.STGSD..S
Retrocopy NSTERAITIAGIPQSITECVKQICVVMLE----SPP<KGLIIPYRPKPSSSPVIFAGNQDRCSTGSDGVS

Parental  FPHTTSM
          FPHTT..
Retrocopy FPHTTTV

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	0.39 RPM	293.06 RPM
SRP012922_cerebellum	0.00 RPM	275.08 RPM
SRP012922_heart	0.00 RPM	145.48 RPM
SRP012922_kidney	0.00 RPM	473.12 RPM
SRP012922_liver	0.15 RPM	279.74 RPM
SRP012922_lung	0.31 RPM	371.27 RPM
SRP012922_quadricep_muscle	0.17 RPM	231.76 RPM
SRP012922_spleen	0.23 RPM	350.82 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_1672 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 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672 , retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,