RetrogeneDB ID: retro_dnov_2237

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_57818:3396..5347(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000000017
• Aliases: None
• Description: None

Sequence

>retro_dnov_2237
ATGAGTGGAGAATCTCAAGTCCACATTTTTGGGGGGGGGGCCCCAGCTGTTCCATTGAAAATGACAGCATCACAGGAACC
AGCTTCTTTAATAGCCACTCCTGAGCCCTGGGGAAAAAATTCAGTTTTTGTGCAGCCAGCACCCTTTACCTGTGAAGACT
GACAGCTGCGAGCACCGAAACCTCAAAGAGCAAATCCGGGAAGCTACAGGTTCTGCAGAGCTTCTTCGCGGTGGCGTGGT
GGCGAGCTCTAGGACTAAATCTGCTCCTTTGAGAGATGACTCTCCACGCTGTATTTCTGAAGCACAGAATATAAAGTTCC
AGAAAAGTCGCTCCTCAGGGGTGAGTGATGTAGCTAACTGTGGTGCGCAGGTGCGTGACCTTGAGGGCGGCGTTCAGCCT
TTAACTGCGGGTGAAACGCCGCGACAGCTTCCGGGTGAGAATGAGATCCCGGAAGGACAGCACAGCGAGCCGTCAGGTAT
CCGCGGTGAGCATGTGAGCGTCTGTCCTCACGGGCAGCTCGTAGAGGCACAGCTGTTTTGGGTTTGGTCTGTAGTACCAG
ACAGACTAGGAGAGGGCCAGGAGCTCTAGAAGCAGAGTGTGTGCCTCGTGAAGCACAAAACCGGCGTCCGCAGTGCTTTC
CCTCGAGAACGGCAGATGAGCCAGGATCTAACGGAGCAGTTCGCCGGGTCTCAGCCTGCGAAGTATCTACCGACGCTGAA
TTTCTAAGTGCGCTGGCCTCCAGCCAGATTGCTCTTTTAGCTCAAAGGCAGCATAAAGGGCAGGATTCTGCAAATAAAGG
AGCCATACCCATGGAGAGTGAACCAAGGGCAAGTCAAGGGGATGAAAGGGTCACTGACGACAACCTGCCTCCATCCAGCG
ATGGAGCATATGGGAACGGACAAGAGCAAGCACGTTCCCTTGAACTTTTTAGTCCTGTTTGTCCCGAAACAGTAAGTAGC
CACGTTCACGTAAATGCCGGTAAAGGTCTTGAAGAAAATACTGCATCTCAGGAACTCTTCAGTTCTGAAGATAAACCGCC
TCCCACTGAGATAATGCTTTGAACCCTGTGGCTCGGGAATACTGTGCTCCCAACGGAGTGCCTTCCGTCCCAGCTCTCCC
AAGAGAAGCAGGAGCTCGGAAGATAAACTGGGCCATTCTAAGGCTCCGACGCGAGGCCTCCCAGTATCTGAGAAAACTAA
GTTGCTGTCTCACGCAGAGGATCCTGCTGTCACAGTGGGCCCGAGCAATGCCTCTGAATTTAAGCGTTTTAAAAAAACGT
CATTGATAAACTGTGATTATAAAAGTTGGAAGTATAATTGTCTAGTCATGGTGTTATTGCCATGTTATGTGAAAGAAATA
TGCATAAAATCAGGACCAAGTTCTGGCTCTAAAGTACCTTTGGCAACAATGGTAGTCATAGACCAATTAGAAGCGAGGAA
GAAGGTTTTTCTGTGGAGGACTGCCGCATTTTGGGCACTTACAGTGTTTCCTGGAGACATAATTTTGCTCACAGATGTTA
CCGTTCGTGAGGATCAATGGGCTGGGGATATAGTACTTCAGACAACTTTCACCAGTCAGTTATTAAATCTTGGGAGTTAT
TCTTCTGTTCAGCCTGAAGAATACTCTGGCGTCATCAGTGCCGTGGTTCTTCGAGGCTTACTGGCGTATGCGTCTTCAGA
GCATCCCCACCTCGGAGCTCTTCCTCGGAGGCCGCCTCAGAACGTGAACAGTGTGGAGTTCGTAGAACTGGAGCGGCTTC
AGCCTGACGTTTTGGTCCATGTGATACTAAGTGTTGTTGATATCACTGTACTAACAGAGGCATCATACAATTACAGAGGA
CAGAAGCAAAGGAAAGTTATGCTAACGGTGGAACAAGCCCAAAGTCAACATTACGTGCTTGTCTTGTGGGGTCCTGAAGA
GGCCTGGCACCCTCAACTTCAAAGGAGAAAA

Alignment

ORF - retro_dnov_2237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGKSQVHIFFGA-PAVPLKMTASQEPASIIPTPEPW-RKIQFLCSQHSLPVKDDSCKHRNLKEQVREAT
          MSG.SQVHIF....PAVPLKMTASQEPAS.I.TPEPW..KIQFLCSQH.LPVK.DSC.HRNLKEQ.REAT
Retrocopy MSGESQVHIFXXXXPAVPLKMTASQEPASLIATPEPW>EKIQFLCSQHPLPVKTDSCEHRNLKEQIREAT

Parental  GSAELLRGGFVASSRTKSPPLRDDSRRCISEAQNIKFQKSRSSGVSDVANCGVQVRELEGGVQPLTAGET
          GSAELLRGG.VASSRTKS.PLRDDS.RCISEAQNIKFQKSRSSGVSDVANCG.QVR.LEGGVQPLTAGET
Retrocopy GSAELLRGGVVASSRTKSAPLRDDSPRCISEAQNIKFQKSRSSGVSDVANCGAQVRDLEGGVQPLTAGET

Parental  PRQLPGENEIPEGQHSDPSGICSQQ-CEHLSSQAARRYTAVLDLVCSTRQTKRGPGALEAECVPHEIQNQ
          PRQLPGENEIPEGQHS.PSGI.....CE.LSS.AARR.TAVL.LVCSTRQT.RGPGALEAECVP.E.QN.
Retrocopy PRQLPGENEIPEGQHSEPSGIRGEH<CERLSSRAARRGTAVLGLVCSTRQTRRGPGALEAECVPREAQNR

Parental  RPQCFPSRTVDEPGSNGAVSQVSACEVSTDTEFLSILASSQIALLAQRQHKGQDSANKGAIPMESEPRAS
          RPQCFPSRT.DEPGSNGAV..VSACEVSTD.EFLS.LASSQIALLAQRQHKGQDSANKGAIPMESEPRAS
Retrocopy RPQCFPSRTADEPGSNGAVRRVSACEVSTDAEFLSALASSQIALLAQRQHKGQDSANKGAIPMESEPRAS

Parental  EGDERVTDDNLPPSRDGAYGNGQEQAHSLELFSPVCPETVSSHIHINAGKGLEENTAFQELFSSEDKLPP
          .GDERVTDDNLPPS.DGAYGNGQEQA.SLELFSPVCPETVSSH.H.NAGKGLEENTA.QELFSSEDK.PP
Retrocopy QGDERVTDDNLPPSSDGAYGNGQEQARSLELFSPVCPETVSSHVHVNAGKGLEENTASQELFSSEDKPPP

Parental  TEI-CIEPCGSGILCSQQSAFCPSSPKRSRSSEEKLGHSKAPSRGLPVSEKTKLLSHTEDPAVTVGPSNA
          TEI.C.EPCGSGILCSQ.SAF.PSSPKRSRSSE.KLGHSKAP.RGLPVSEKTKLLSH.EDPAVTVGPSNA
Retrocopy TEI>CFEPCGSGILCSQRSAFRPSSPKRSRSSEDKLGHSKAPTRGLPVSEKTKLLSHAEDPAVTVGPSNA

Parental  SEFKRFKKTSLIKNCDYKSWKYNCLVMVLLPCYVKEINIKSGPSSGSKVPLATMVVIDQSETRKKVFLWR
          SEFKRFKKTSLI.NCDYKSWKYNCLVMVLLPCYVKEI.IKSGPSSGSKVPLATMVVIDQ.E.RKKVFLWR
Retrocopy SEFKRFKKTSLI-NCDYKSWKYNCLVMVLLPCYVKEICIKSGPSSGSKVPLATMVVIDQLEARKKVFLWR

Parental  TAAFWALTVFPGDIVLLTDVTIREDQWAGDTVLQTTFTSQLLNLGSYSSVQPEEYSGVVSAVVLRGLLAY
          TAAFWALTVFPGDI.LLTDVT.REDQWAGD.VLQTTFTSQLLNLGSYSSVQPEEYSGV.SAVVLRGLLAY
Retrocopy TAAFWALTVFPGDIILLTDVTVREDQWAGDIVLQTTFTSQLLNLGSYSSVQPEEYSGVISAVVLRGLLAY

Parental  ASSKHPHLAALPRRQPQNVSSVEFVELERLQPDVLVHVILRVVDISVLTEASYSYRGQKQRKAMLTVEQA
          ASS.HPHL.ALPRR.PQNV.SVEFVELERLQPDVLVHVIL.VVDI.VLTEASY.YRGQKQRK.MLTVEQA
Retrocopy ASSEHPHLGALPRRPPQNVNSVEFVELERLQPDVLVHVILSVVDITVLTEASYNYRGQKQRKVMLTVEQA

Parental  QGQHYMLVLWGPGEAWHPQLQRRK
          Q.QHY.LVLWGP.EAWHPQLQRRK
Retrocopy QSQHYVLVLWGPEEAWHPQLQRRK

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	1.17 RPM	11.86 RPM
SRP012922_cerebellum	5.09 RPM	60.49 RPM
SRP012922_heart	1.16 RPM	12.76 RPM
SRP012922_kidney	2.46 RPM	28.75 RPM
SRP012922_liver	2.79 RPM	17.80 RPM
SRP012922_lung	2.75 RPM	27.34 RPM
SRP012922_quadricep_muscle	2.94 RPM	33.58 RPM
SRP012922_spleen	2.63 RPM	36.97 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_2237 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011809	1 retrocopy	retro_chof_1126,
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237 ,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073, retro_nleu_2157, retro_nleu_840,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,