RetrogeneDB ID: retro_dnov_1618

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24810:42057..42908(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000322
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSDNOG00000007765
• Aliases: None
• Description: cyclin H [Source:HGNC Symbol;Acc:1594]

Sequence

>retro_dnov_1618
GTTCTTCCCAATGATCTAGTCTTTCTTAACCTCATGAAGAAATGGTACTCTGCAAATACTATGAGAAAAATTATTGGAAT
TCTGTTCAGTGTTTAAGCCAACAATGCCAAAGACTGTTGTGGGTACAGCGTGTATGTATTTCAAGCGTTTTTATCTTAAT
AACTCAGTAATGGAATACCACCCCCGAATAATAATGCTCACTTGTGCTTTTCTGGGCTGCAAAGTCGATGAGTTCAATGT
CTCTAGTCCACAATTTGTTGGAAATCTTCGAGAGAGTCCTCTTGGACAGGAGAAGACACTAGAACAGATTTTGGAATGTG
AACTACTACTGATACAGCAACTTAATTTCCACCTTATTGTCCACAATCCTTACAGACCGTTTGAGGGCTTCCTCATTGAT
TTAAAGACTCCTTATCCCATGTTGGAGAACCCTGAGTTTTTGAGAAAACAGCTGATGACTTACTTAATAGAGTTGCATTG
ACGGATGCTTACCTTTTATATACACCTTCCCAGATTGCTCTGACGAGCTATTATATCTAGTGCTTCCAGGGCTGGAAATT
ACTATGGAAAGTTATTTATCAGAGAGCCTTATGCTGAAAGAGAATAGAACTTGCTTCTCACAGTTTCTAGAGATAATGAA
AAGCATGAGAAACTTGGTAAAAAAATATGAACCACCCAGATCGGAAGAAGTTGCTGTTCTGAAACAGAAGTTGGAAAGAT
GTCACTCTGCTGAGCTTGCACTTAATGTAATTACGAAGAAGAGGAAGGGCTATGAAGACGATGATTATATCTCAAAGAAA
TCCAAACATGAGAAGGAAGAATGGACTGATGACGACCTGGTAGATTCTCTC

Alignment

ORF - retro_dnov_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VLPNDLVFLE-PHEEMVLCKYYEK-RLLEFCSVFKPTMPKSVVGTACMYFKRFYLNNSVMEYHPRIIMLT
          VLPNDLVFL..PHEEMVLCKYYEK..LLEFCSVFKPTMPK.VVGTACMYFKRFYLNNSVMEYHPRIIMLT
Retrocopy VLPNDLVFLN<PHEEMVLCKYYEK<KLLEFCSVFKPTMPKTVVGTACMYFKRFYLNNSVMEYHPRIIMLT

Parental  CAFLACKVDEFNVSSPQFVGNLRESPLGQEKRVEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTR
          CAFL.CKVDEFNVSSPQFVGNLRESPLGQEK..EQILE.ELLLIQQLNFHLIVHNPYRPFEGFLIDLKT.
Retrocopy CAFLGCKVDEFNVSSPQFVGNLRESPLGQEKTLEQILECELLLIQQLNFHLIVHNPYRPFEGFLIDLKTP

Parental  YPMLENPEFLR-KTADDFLSRVALTDAYLLYTPSQIALT-AIISSASRAG-ITMESYLSESLMLKENRTC
          YPMLENPEFLR.KTADD.L.RVALTDAYLLYTPSQIALT.AIISSASRAG.ITMESYLSESLMLKENRTC
Retrocopy YPMLENPEFLR<KTADDLLNRVALTDAYLLYTPSQIALT>AIISSASRAG>ITMESYLSESLMLKENRTC

Parental  LSQLLEIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYISKKSKHEEEEW
          .SQ.LEIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYISKKSKHE.EEW
Retrocopy FSQFLEIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYISKKSKHEKEEW

Parental  TDDDLVDSL
          TDDDLVDSL
Retrocopy TDDDLVDSL

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	0.58 RPM	8.75 RPM
SRP012922_cerebellum	3.71 RPM	12.92 RPM
SRP012922_heart	2.78 RPM	8.82 RPM
SRP012922_kidney	1.10 RPM	12.05 RPM
SRP012922_liver	0.31 RPM	3.56 RPM
SRP012922_lung	2.14 RPM	11.45 RPM
SRP012922_quadricep_muscle	1.04 RPM	10.73 RPM
SRP012922_spleen	2.86 RPM	11.90 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_1618 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618 ,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,