RetrogeneDB ID: retro_dnov_2337

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_65445:1772..2666(-)
• 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_2337
AAAACAACTCAGAGGAAGAAACAAATCGCTATGGGAAGCAAGAAATTCAATGCGGCTCCCAAAAAGGGAATTCATTTCCT
AAAGGAACAATGACCTGCTGCAGCGTTCCCCAGAAGACGTAGCCCGGTTCCTTTGAAAAGAAAGCCTACAGAAGACCCTC
ATCTGGCACTCGGTGGGCAAAAGGGACGGATCTCCCTTTCAGGTTCTTCAGGCCTCCATGGAGCTCCACGCGTTGCTGAG
CTCGACCTGGTACCAGCCTAAGGCAGATGTTGGGGAGCTGTTGACATCCAGGGGAGACTCGGAGCACTGATGGCAGGATG
GAGGCCTTGGTGGCATGCTGCTCCCCGTGTCACCCCGAGGTCTTCCAGCCCACAGACACGTGCTCCACACTGTCCTTCAC
CTCATCCTGCTCAACACCAGCCTCCACAACCACATCGTGCGGGACAAGCCCACGGCCGAGCGCTCAGGCCCCAGGAGCAG
GGCACCCAGGAGGGCAGGGACCTGCCTGAGCAGGGGCTGCAGAATTTATATCAAAGTGTTCAACACGAACCGTTTACAGC
CCAGAGGACAATGGCAATGCCCTGAGGCACATGTTCTTCCATCCTGAACCCGGGGGCTGGCTCCTGACGCCCGGGGGCGA
GTGGAGCCCTGGAAGGGCTGCTGGTTCATCCTGTCCCTCTACCGCCCCTACTTCCTCAAACACACACCAGGTAAGGAGCC
CAGGCGGGGCAACTCGCTGGAAACCCTCAGCATAAGAGAGCTGCAAGACCTCCTGCGCAAGCCCAACTGTTTTGAGCTTC
ATACCCCGAGCCACAAAGGGCAAGTTATCCAAGCCTGGAAGACAGAAGCAGAGGACTCAGGGCTGGAGGCAGCCACGTGG
TGCTCCGCATCTCA

Alignment

ORF - retro_dnov_2337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.58 %
• Parental protein coverage: 74.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

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

Parental  LHAFVELH-EFTDLNLVQA-LRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNSGVFQSTDTCYVLSFA-I
          L.A..ELH.....L.LV.A.LRQ.L.S...PGE....D..MEA.......C...VFQ.TDTC..LSF...
Retrocopy LQASMELH<RVAELDLVPA<LRQMLGSC*HPGETRSTDGRMEALVACCSPCHPEVFQPTDTCSTLSFT<L

Parental  IMLNTSLHNPNVKDKPTVERFIAMNR-GINDGGDLPEELLRNLYESIKNEPFKI-PEDDGNDLTHTFFNP
          I.LNTSLHN..V.DKPT.ER.....R.G...G.DLPE..L.NLY.S...EPF...PED.GN.L.H.FF.P
Retrocopy ILLNTSLHNHIVRDKPTAERSGPRSR<GTQEGRDLPEQGLQNLYQSVQHEPFTA<PEDNGNALRHMFFHP

Parental  DREGWLLKLAGG-RVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVED-SKKPNCFELYIP
          ...GWLL...GG.RV..WK..WFIL.....Y....T..KEPR....LE.LSIRE..D...KPNCFEL..P
Retrocopy EPGGWLL-TPGG<RVEPWKGCWFILSLYRPYFLKHTPGKEPRRGNSLETLSIRELQDLLRKPNCFELHTP

Parental  DNKDRVIKACKTEADGRVVE-GNHTVYRIS
          ..K..VI.A.KTEA.....E.G.H.V.RIS
Retrocopy SHKGQVIQAWKTEAEDSGLE<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_2337 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 ,