RetrogeneDB ID: retro_dnov_1148

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_154155:532..1480(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025805
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSDNOG00000014002
• Aliases: None
• Description: eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]

Sequence

>retro_dnov_1148
GACAAGACAAGCTCTTCCTACTATGGGGAACAAATGCTGCACTACATTGCAACAAATGGAGAAAGTGCTATAGTGCAATT
ACCAAAAAATGGTCCCATTTATGATGTAGTATGGAACTCTAGTTCCACTCAATTTTGTGCTGTTTATGGTTTTATGCCTG
CCAAAGCAACAGTTTTCAACTTGAAATGTGATCCTGTGTTTGATTTTGGAACTGGCCCTCATAATGCAGCCTTCTATGGC
CCTCATGGACATATATTAGTACTAGCTGGATTTGGAAATCTGAGGGGACAAATGGAAGTATGGGATGTTAAAAACTACAA
ACTTATTTCTAAACCAGTGGCCTTTGATTCTAAATATTTTGCTTGGTACCCAGATGGTGAGCATATTTTGACCACCACGT
GTGCTCCCAGGTTATGTGTTAATAATGGGTACAAGATTTGGCATTATACTGGCTCTGTCTTGCACAAATATGATGTGCCA
TCAAATGCAGAAATTTGGCAGGTTTCTTGGCAGCCATTTTTGGATGAAATATTTCCAGCAAAAAAAAAAATAACTTACCA
AGCAGTTCCAAGTGAAGTACCCAATGAGGAACCTAAAGTTACAACGGCTTATAGACCCCCAGCTATAAGAAATAAACCAA
TCACCAATTCCAAACTGCATGAGGATGAACCACCTCAGAATATGAAGCCACAACCAGGAAATGATAAGGCATTATCAAAA
ACAGCCCTTAAAAATCAAAGGAAGCATGAAGCCAAGAAAGCCGCAAAGCAGGAAGCAAGAAGTGACAAGAGTCCAGATTT
GGCCCCTCCTGCCCCACAGAGCATACGACAAAATACTATCTCTCAGTCAAATTTGGGAGACCCAGAGATAGACAGAAAAA
TCAAGAACCTTAAGAAGAAACTAAAAGCAATTGAACAACTGAAAGAACAAGCAGCAAGTGGAAAACAG

Alignment

ORF - retro_dnov_1148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.19 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKTGASYYGEQTLHYIATNGESAVVQLPKNGPIYDVVWNSSSTEFCAVYGFMPAKATVFNLKCDPVFDFG
          DKT..SYYGEQ.LHYIATNGESA.VQLPKNGPIYDVVWNSSST.FCAVYGFMPAKATVFNLKCDPVFDFG
Retrocopy DKTSSSYYGEQMLHYIATNGESAIVQLPKNGPIYDVVWNSSSTQFCAVYGFMPAKATVFNLKCDPVFDFG

Parental  TGPRNAAFYSPHGHILVLAGFGNLRGQMEVWDVKNYKLISKPVASDSTYFAWCPDGEHILTATCAPRLRV
          TGP.NAAFY.PHGHILVLAGFGNLRGQMEVWDVKNYKLISKPVA.DS.YFAW.PDGEHILT.TCAPRL.V
Retrocopy TGPHNAAFYGPHGHILVLAGFGNLRGQMEVWDVKNYKLISKPVAFDSKYFAWYPDGEHILTTTCAPRLCV

Parental  NNGYKIWHYTGSVLHKYDVPSNAEIWQVSWQPFLDGIFP-AKKITYQAVPSEVPSEEPKVTTAYRPPALR
          NNGYKIWHYTGSVLHKYDVPSNAEIWQVSWQPFLD.IFP.....TYQAVPSEVP.EEPKVTTAYRPPA.R
Retrocopy NNGYKIWHYTGSVLHKYDVPSNAEIWQVSWQPFLDEIFPXXXXXTYQAVPSEVPNEEPKVTTAYRPPAIR

Parental  NKPVTNSKLHED-PPQNM-PQ-GNDKPLSKTALKNQRKHEAKKAAKQEARSDKSPDLAPPAPQSTPQNII
          NKP.TNSKLHED.PPQNM.PQ.GNDK.LSKTALKNQRKHEAKKAAKQEARSDKSPDLAPPAPQS..QN.I
Retrocopy NKPITNSKLHEDEPPQNMKPQPGNDKALSKTALKNQRKHEAKKAAKQEARSDKSPDLAPPAPQSIRQNTI

Parental  SQSTSGDPEIDKKIKNLKKKLKAIEQLKEQAASGKQ
          SQS..GDPEID.KIKNLKKKLKAIEQLKEQAASGKQ
Retrocopy SQSNLGDPEIDRKIKNLKKKLKAIEQLKEQAASGKQ

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	12.25 RPM	42.78 RPM
SRP012922_cerebellum	9.07 RPM	30.52 RPM
SRP012922_heart	3.71 RPM	23.67 RPM
SRP012922_kidney	16.98 RPM	39.15 RPM
SRP012922_liver	6.50 RPM	34.52 RPM
SRP012922_lung	14.36 RPM	45.36 RPM
SRP012922_quadricep_muscle	16.27 RPM	63.87 RPM
SRP012922_spleen	13.16 RPM	50.25 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_1148 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148 ,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,