RetrogeneDB ID: retro_dnov_600

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6684:147767..148461(-)
• Located in intron of: ENSDNOG00000004626

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX7
• Ensembl ID: ENSDNOG00000000295
• Aliases: None
• Description: syntaxin 7 [Source:HGNC Symbol;Acc:11442]

Sequence

>retro_dnov_600
GTGGAAATACAAAGGACTCCTGAATCAAACTGGGACCTCCCCCAAGATTCTCCTGAATTAAGCCAACAACTGCAAAAGAA
GCAGCAGTACACTAACCAACTTCCCCAAAGAAACAGATAAATAACTGAGGAGTTTGGATCTCTTTCTACCACCCCCAGTG
GCAGGGACAAAGGGAAGATACAAAAGGACTGCTTAGTGGTGGAATTCACATCCTCACTGACAAGCTTTCAGAAGGTCAAG
AGGCAAACTGCTGAGAGAGAGGAGTTTGTTGCTCCAGGAAGAGTCAGCTCCAGAGTATCTGGGGGTTTTCGTGAAGACAG
TTCAAAAGAAAGGAATCTTATATCCTGGGAAAGCCAAACTCAACCCTCAAATGCAGGTACAAAATGAAGAAATTAGAGAT
GATGACCCCTCCCTCATTCATGAGAGAGAGTCTTCTGTTAGATACCTGGAAGCTGATACTCTGGGTATTAATGAAACATT
TAAAGATTTGGGACTGATGACTCATGAACAAGGAGATATGATAGATAGCATAAGAGCCAATGTAGAAAATGCTGAGGTGC
ACATTCAGCAAGCAAATCAGCAGCTGTCAAGGGCAGCAGATTACCAGTGCAAATCCAGAAAAACCCTGTGCATCATCATT
TTTATCCTTGTCATTGGAACTATGATTATCAGTCTCATCATATGGGGAGGGAAA

Alignment

ORF - retro_dnov_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 88.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VEIQRTL-NQLGTPQDSPELRQQLQQKQQYTNQLA-KETDKYIK-EFGSLPTTPSEQRQRKIQKDRLVAE
          VEIQRT.......PQDSPEL.QQLQ.KQQYTNQL..KETDK....EFGSL.TTPS.....KIQKD.LV.E
Retrocopy VEIQRTPESNWDLPQDSPELSQQLQKKQQYTNQLP>KETDK*LR<EFGSLSTTPSGRDKGKIQKDCLVVE

Parental  FTTSLTNFQKVQRQAAEREKEFVARVRASSRVSGGFPEDSSKERNLVSWESQTQP-QVQVQDEEITEDDL
          FT.SLT.FQKV.RQ.AERE.EFVA..R.SSRVSGGF.EDSSKERNL.SWESQTQP.Q.QVQ.EEI..DD.
Retrocopy FTSSLTSFQKVKRQTAERE-EFVAPGRVSSRVSGGFREDSSKERNLISWESQTQP>QMQVQNEEIRDDDP

Parental  RLIQERESSIRQLEADIMDINEIFKELGMMIHEQGDMIDSIEANVENAEVHVQQANQQLSRAADYQRKSR
          .LI.ERESS.R.LEAD...INE.FK.LG.M.HEQGDMIDSI.ANVENAEVH.QQANQQLSRAADYQ.KSR
Retrocopy SLIHERESSVRYLEADTLGINETFKDLGLMTHEQGDMIDSIRANVENAEVHIQQANQQLSRAADYQCKSR

Parental  KTLCIIIFILVIGVVIIGLIIWGVK
          KTLCIIIFILVIG..II.LIIWG.K
Retrocopy KTLCIIIFILVIGTMIISLIIWGGK

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	37.14 RPM
SRP012922_cerebellum	0.00 RPM	38.22 RPM
SRP012922_heart	0.00 RPM	11.60 RPM
SRP012922_kidney	0.00 RPM	32.31 RPM
SRP012922_liver	0.00 RPM	5.26 RPM
SRP012922_lung	0.00 RPM	76.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.90 RPM
SRP012922_spleen	0.11 RPM	53.68 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_600 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	ENSCHOG00000010117	3 retrocopies	retro_chof_1503, retro_chof_2631, retro_chof_829,
Dasypus novemcinctus	ENSDNOG00000000295	1 retrocopy	retro_dnov_600 ,
Felis catus	ENSFCAG00000002292	1 retrocopy	retro_fcat_977,
Myotis lucifugus	ENSMLUG00000004301	1 retrocopy	retro_mluc_494,
Sarcophilus harrisii	ENSSHAG00000014440	1 retrocopy	retro_shar_430,
Tursiops truncatus	ENSTTRG00000009853	1 retrocopy	retro_ttru_185,