RetrogeneDB ID: retro_dnov_2322

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_6402:25181..26076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYTH1
• Ensembl ID: ENSDNOG00000005074
• Aliases: None
• Description: cytohesin 1 [Source:HGNC Symbol;Acc:9501]

Sequence

>retro_dnov_2322
AAAACAACTCAGAGGAAGAAACAAATCGCTATGGGAAGCAAGAAATTCAATGCGGCTCTCAAAAAGGGAATTCATTTCCT
AAAGGAACAATGACCTGCTGCAGCGTTCCCCAGAAGACGTAGCCCGGTTCCTTTGAAAAGAAAGCCTACAGAAGACCCTC
ATCTGGCACTCGGTGGGCAAAAGGGACGGATCTCCCTTTCAGGTTCTTCAGGCCTCCATGGAGCTCCACGCGTTTGCTGA
GCTCGACCTGGTACCAGCCTAAGGCAGATGTTGGGGAGCTGTTGACATCCAGGGGAGACTCAGAGCACTGATGGCAGGAT
GGAGGCCTTGGTGGCATGCTGCTCCCCGTGTCACCCCGAGGTCTTCCAGCCCACAGACACGTGCTCCACACTGTCCTTCA
CCTCATCCTGCTCAACACCAGCCTCCACAACCACATCGTGCGGGACAAGCCCACGGCCGAGCGCTCAGGCCCCAGGAGCA
GGGCACCCACGAGGGCAGGGACCTGCCTGAGCAGGGGCTGCAGAATTTATATCAAAGTGTTCAACACGAACCGTTTACAG
CCCAGAGGACAATGGCAATGCCCTGAGGCACATGTTCTTCCATCCTGAACCCGGGGGCTGGCTCCTGACGCCCGGGGGCG
AGTGGAGCCCTGGAAGGGCTGCTGGTTCATCCTGTCCCTCTACCGCCCCTACTTCCTCAAACACACACCAGGTAAGGAGC
CCAGGCGGGGCAACTCGCTGGAAACCCTCAGCATAAGAGAGCTGCAAGACCTCCTGCGCAAGCCCAACTGTTTTGAGCTT
CATACCCCGAGCCACAAAGGGCAAGTTATCCAAGCCTGGAAGACAGAAGCAGAGGACTCAGGGCTGGAGGCAGCCACGTG
GTGCTCCGCATCTCA

Alignment

ORF - retro_dnov_2322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.07 %
• Parental protein coverage: 74.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KNMQRNKQVAMGRKKFNMDPKKGIQFLIE-NDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQV
          K..QR.KQ.AMG.KKFN...KKGI.FL.E.NDLL....ED.A.FL.K.E.L.KT.I....G.RD....QV
Retrocopy KTTQRKKQIAMGSKKFNAALKKGIHFLKE>NDLLQRSPEDVARFL*K-ESLQKTLIWHSVGKRDGSPFQV

Parental  LHAFVELHEFTDLNLVQA-LRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNSGVFQSTDTCYVLSFA-II
          L.A..ELH.F..L.LV.A.LRQ.L.S...PGE.Q..D..MEA.......C...VFQ.TDTC..LSF...I
Retrocopy LQASMELHAFAELDLVPA<LRQMLGSC*HPGETQSTDGRMEALVACCSPCHPEVFQPTDTCSTLSFT<LI

Parental  MLNTSLHNPNVKDKPTVERFIAMNR-GINDGGDLPEELLRNLYESIKNEPFKI-PEDDGNDLTHTFFNPD
          .LNTSLHN..V.DKPT.ER.....R.G...G.DLPE..L.NLY.S...EPF...PED.GN.L.H.FF.P.
Retrocopy LLNTSLHNHIVRDKPTAERSGPRSR<GTHEGRDLPEQGLQNLYQSVQHEPFTA<PEDNGNALRHMFFHPE

Parental  REGWLLKLAGG-RVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVED-SKKPNCFELYIPD
          ..GWLL...GG.RV..WK..WFIL.....Y....T..KEPR....LE.LSIRE..D...KPNCFEL..P.
Retrocopy PGGWLL-TPGG<RVEPWKGCWFILSLYRPYFLKHTPGKEPRRGNSLETLSIRELQDLLRKPNCFELHTPS

Parental  NKDRVIKACKTEADGRVVE-GNHTVYRIS
          .K..VI.A.KTEA.....E.G.H.V.RIS
Retrocopy HKGQVIQAWKTEAEDSGLE<GSHVVLRIS

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	14.20 RPM
SRP012922_cerebellum	0.00 RPM	23.37 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.00 RPM	3.29 RPM
SRP012922_liver	0.00 RPM	4.64 RPM
SRP012922_lung	0.00 RPM	17.87 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.00 RPM	33.54 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_2322 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005074	3 retrocopies	retro_dnov_1437, retro_dnov_2322 , retro_dnov_2337,