RetrogeneDB ID: retro_dnov_1790

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_30482:12493..13162(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPHLN1
• Ensembl ID: ENSDNOG00000002007
• Aliases: None
• Description: periphilin 1 [Source:HGNC Symbol;Acc:19369]

Sequence

>retro_dnov_1790
ATATGGTCTGAGGGATGATATGACTACAAAAGGTTTCCAAGAGAAAGATTACGTCCTAGGAGTCACCCCAATGATGGCGT
CCATAGAGCAGTTAATATTGTGCCAAAGAAACCACCACTGCTAGAAAGACCTGGTGAAGGAAGCTGCAATAGATGTAACA
GTTATGTTAATTACTGAGACCATGATGAGGGCCACAGTTTTTATCAGGATGGAAGAAGTGGTCCTCCTCACAGAGGGGAT
GAATCTGGCTCTAGATGGCTAAGAGATGATCATTCTGCAAGTCGACAGCCTGAATACAGGGACATGAGAGATGGCTTTAG
AAGAAACAGTTTCTATTCTTTCCATTATGTGAGAGATGGGTCTCCTCATAAAGAGGACAATTCTTATCTCACAGAATCAC
CTGTAGGTGGAAAGAAGTCTCCTCACAGCAGATCTGGCTCCAGTAGCAGCAGAAGCTACTCTCCAGAAAAAAGCAAAACA
TACTCTTTCCATCAATCTCAACATAGAAAGTCCATGCATGCAGGTGCATCCTACAAATGGCAGAATGAAGGAAAGCCAGA
ATGAGGTAAAGAGAGACCTGCCCAGTCTTTGAAAACATCAGGAGATACTTCATCCTCAAGTTCTTCAGCAGTTACTTCAT
CAAAGATGTCAGACAAGCCCATGTTGCTT

Alignment

ORF - retro_dnov_1790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 73.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWSEGRYDYERLPRERLPPRSHPSDGVHRVVNIVPKKPPLLDRPGEGSYNRYNSHVDYRDYDEGRSFSHD
          .WSEG.YDY.R.PRERL.PRSHP.DGVHR.VNIVPKKPPLL.RPGEGS.NR.NS.V.Y.D.DEG.SF..D
Retrocopy IWSEG*YDYKRFPRERLRPRSHPNDGVHRAVNIVPKKPPLLERPGEGSCNRCNSYVNY*DHDEGHSFYQD

Parental  RRSGPPHRGDESSYRWPRDDHSASRQPEYRDVRDGFRRKSFYSSHYARDRSPHKRDNSYLRESPVGRKDS
          .RSGPPHRGDES..RW.RDDHSASRQPEYRD.RDGFRR.SFYS.HY.RD.SPHK.DNSYL.ESPVG.K.S
Retrocopy GRSGPPHRGDESGSRWLRDDHSASRQPEYRDMRDGFRRNSFYSFHYVRDGSPHKEDNSYLTESPVGGKKS

Parental  SHSRSGSSVSSRSYSPERSKTYS-HQSQHRKSVRAGASYKRQNEGKPERGKERPLQAMKTSGDTSPSSSS
          .HSRSGSS.SSRSYSPE.SKTYS.HQSQHRKS..AGASYK.QNEGKPE.GKERP.Q..KTSGDTS.SSSS
Retrocopy PHSRSGSS-SSRSYSPEKSKTYSFHQSQHRKSMHAGASYKWQNEGKPE*GKERPAQSLKTSGDTSSSSSS

Parental  AVTSSKVLDKPSRL
          AVTSSK..DKP..L
Retrocopy AVTSSKMSDKPMLL

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	13.81 RPM
SRP012922_cerebellum	0.00 RPM	8.52 RPM
SRP012922_heart	0.00 RPM	4.87 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	5.57 RPM
SRP012922_lung	0.00 RPM	11.30 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.00 RPM	19.12 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_1790 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790 ,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,