RetrogeneDB ID: retro_dnov_1966

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39346:3108..4005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSDNOG00000005984
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_dnov_1966
ATGTCTCTGCATCAGTTTTTACTAGAGCCAATCACCTGTCATGCTTGGAACAGGGATCGTACACAGATTGCCCTTAGCCC
CAATAACCATGAAGTTCACATCTATAAGAAGAATGGGAGCCAGTGGGTAAAAACGCACGAACTCAAGGAGCACAATGGAC
ACATCACAGGTATTGACTGGGCTCCCAAGAGTGACCGCATTGTCACTTGCGGGGCAGATCGCAATGCTTATGTCTGGAGT
CAGAAAGATGGTATCTGGAAGCCGACCCTGGTGATCCTGAGAATTAATCGTGCAGCCACTTTTGTGAAGTGGTCCCCTCT
AGAGAACAAATTTGCTGTGGGAAGTGGAGCATGGCTCATTTCTGTTTGTTACTTCGAGTCTGAAAATGACTGGTGGGTAA
GCAAGCACATTAAAAAGCCTATTCGTTCCACGGTCCTCAGCTTGGATTGGCATCCCAACAATGTTTTGCTGGCAGCAGGA
TCCTGTGACTTCAAATGCAGAGTGTTTTCTGCCTACATTAAAGAAGTGGATGAAAAGCCAGCCAGTACACCATGGGGCAG
CAAAATGCCTTTTGGCCAGCTGATGTCAGAATTTGGTGGCAGTGGCACCGGTGGTTGGGTCCACGGGGTCAGCTTTTCTG
CCAGTGGGAGCCGCCTGGCCTGGGTCAGCCATGACAGCACTGTGTCTGTAGCTGATGCCTCAAAAAGTGTGCAGGTTTCA
ACTCTGAAAACGGAGTTCCTGCCACTCCTGAGTGTATCATTTATCTCCGAGAATAGTGTGATAGCTGCTGGCCACGACTG
CTGCCCAATGCTCTTTAATTACGATGACCGTGGCTGCTTGACCTTCGTCTCCAAACTAGACCTTCCAAAACAGAGCATCC
AGGGCAACATGTCGGCA

Alignment

ORF - retro_dnov_1966 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.0 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKTHELKEHNGHITGIDWAPKSDRIVTC
          MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKTHELKEHNGHITGIDWAPKSDRIVTC
Retrocopy MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKTHELKEHNGHITGIDWAPKSDRIVTC

Parental  GADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKP
          GADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGA.LISVCYFESENDWWVSKHIKKP
Retrocopy GADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGAWLISVCYFESENDWWVSKHIKKP

Parental  IRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGV
          IRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGV
Retrocopy IRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGV

Parental  SFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVSFISENSVVAAGHDCCPMLFNYDDRGCL
          SFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVSFISENSV.AAGHDCCPMLFNYDDRGCL
Retrocopy SFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVSFISENSVIAAGHDCCPMLFNYDDRGCL

Parental  TFVSKLDLPKQSIQRNMSA
          TFVSKLDLPKQSIQ.NMSA
Retrocopy TFVSKLDLPKQSIQGNMSA

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	36.75 RPM	82.84 RPM
SRP012922_cerebellum	23.78 RPM	49.63 RPM
SRP012922_heart	5.57 RPM	9.98 RPM
SRP012922_kidney	14.78 RPM	42.99 RPM
SRP012922_liver	8.05 RPM	18.58 RPM
SRP012922_lung	24.74 RPM	56.81 RPM
SRP012922_quadricep_muscle	3.12 RPM	9.35 RPM
SRP012922_spleen	29.07 RPM	61.58 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_1966 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 7 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005984	5 retrocopies	retro_dnov_1615, retro_dnov_1839, retro_dnov_1966 , retro_dnov_2257, retro_dnov_941,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Sus scrofa	ENSSSCG00000007609	1 retrocopy	retro_sscr_387,
Tursiops truncatus	ENSTTRG00000003002	4 retrocopies	retro_ttru_1621, retro_ttru_1838, retro_ttru_575, retro_ttru_853,