RetrogeneDB ID: retro_dnov_826

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_111386:3129..3649(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSDNOG00000004429
• Aliases: None
• Description: SPC25, NDC80 kinetochore complex component [Source:HGNC Symbol;Acc:24031]

Sequence

>retro_dnov_826
ATGATAGAGTACGAACTGGCACTATTTGATAAAAGCATAAATGAATTTTGGAATAAATTGAAGAGGACTGTCAGTGACAA
CTCCTGTCAGATGGTGGGGCTAAGAGATACCTACAAGGACTCCGTTAAAGCATTTGCAGAGAAGCTGTCTGTGAAATTAA
AGGAAGAAGACAGAATGTTTGAGATGTTCCTGGAATATCAAAATCAGATCTGGAGGCAAAATAAGCTCATTCAGGAAAAA
AAAAGATAACTTGTTAAAGTTGATTGCTGAAGTAAAAGACAAAAAGCAAGAAGTGGAAGTATTGACTGCAAATATCCAGG
ATCTTAAGGAAGAATATGCAAAGAAGAAGGAAACAATTTCTGCTACAAACAAAGCCAATGAAGAGAGGTTGAAAAGGCTG
CAGAAATCTGAAGACTTATATAAAGATAGACTTGGACTAGAAATTAGAAAAATTTATGGTGATAAATTACAGTTTATTTT
CACTAATATTGACCCTAAGCATCCTGAGAATCCATTTATA

Alignment

ORF - retro_dnov_826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.38 %
• Parental protein coverage: 76.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIEDELALFDKSINEFWNKFKGTVSDNSCQMVGLRDTYKDSIKAFAEKLSVKLKEEDRMVEMFLEYQNQI
          MIE.ELALFDKSINEFWNK.K.TVSDNSCQMVGLRDTYKDS.KAFAEKLSVKLKEEDRM.EMFLEYQNQI
Retrocopy MIEYELALFDKSINEFWNKLKRTVSDNSCQMVGLRDTYKDSVKAFAEKLSVKLKEEDRMFEMFLEYQNQI

Parental  WRQNKLIQEKK-DNLLKLIAEVKDKKQEVEVLTANIQDLKEEYAKKKETISAANKANEEKLKRLQKSADL
          WRQNKLIQ....DNLLKLIAEVKDKKQEVEVLTANIQDLKEEYAKKKETISA.NKANEE.LKRLQKS.DL
Retrocopy WRQNKLIQXXX>DNLLKLIAEVKDKKQEVEVLTANIQDLKEEYAKKKETISATNKANEERLKRLQKSEDL

Parental  YKDRLGLEIRKIYGDKLQFIFTNIDPKHPETPYM
          YKDRLGLEIRKIYGDKLQFIFTNIDPKHPE.P..
Retrocopy YKDRLGLEIRKIYGDKLQFIFTNIDPKHPENPFI

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	12.06 RPM
SRP012922_cerebellum	0.00 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.27 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.62 RPM
SRP012922_lung	1.83 RPM	1.37 RPM
SRP012922_quadricep_muscle	0.35 RPM	0.17 RPM
SRP012922_spleen	0.34 RPM	17.40 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_826 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541, retro_chof_2326, retro_chof_744,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826 ,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,