RetrogeneDB ID: retro_dnov_2666

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_96326:6360..7054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSCAN4
• Ensembl ID: ENSDNOG00000011483
• Aliases: None
• Description: zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709]

Sequence

>retro_dnov_2666
TTGAGAGGGAACTGGGATTCAAGTGGAAGAATCCTGGAGAAACTCATGGAAGATCTGACCATTGACTGCATGAGGTCACC
TGATTTTGTTCATGTCTACATGCAGGGACAAGAAGCCCACTTCTCAGAAAATATGACCTTAAGGGAACTATTCATCTCAT
GGCAAAAAAATGTCAGCAGGAACCCCAAGAGAAGGGAGCAGGAGGACACCTTTCCATGGTCCCCAAAATAGTCCCCTTCG
AACAGGACAAGCAGAGGAATATCAACAGTTCTGTGATATTCCAATCAAGTAAATGACGGTATTACTAACTGAGTCAATCA
ATGACCTACCCTGGTTATTATTCAGGAAGATAATACCCTAAGCCTGAAGAAGGGTGTGGAACCTGGGAGAACCTGCATAA
CTCCAGAAGAGCAGAGCTTGGCTCCTCCATATCCCAGAAAGGATCCCTAGGATGATCTTCTCAAGATGTCCTTATGGAGG
TGGAACCACAGTTTCTCCCCAGGATAGATCTAGCCATCTCTAAGCCTTTCCCTACCAACCAAAGCAATGATGGAATATAC
AGATGTGGAATAAACCAAGAAAGTGTCCACAGTTACCCAAAATCACATAAGTATGAGAACTGTCCCAGGATCCTTAGGTA
CCAGCTCAGCTAGACACCCACCAGAGAAGACACAAGAATGTGAGATCATTTGTT

Alignment

ORF - retro_dnov_2666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.08 %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKEKWDSSGRNLEKLVGELNDDCMKSPDFVHVHMQGQEALFSENMPLREVIYLME-QMPAGTPRGESMRT
          L...WDSSGR.LEKL...L..DCM.SPDFVHV.MQGQEA.FSENM.LRE........M.AGTPR..S.RT
Retrocopy LRGNWDSSGRILEKLMEDLTIDCMRSPDFVHVYMQGQEAHFSENMTLRELFISWQ>KMSAGTPREGSRRT

Parental  PFQGPQNIPLQTGHGDEYKDDSNIFVKRNQINVNITSQGNQVPY-VVIIQEDDS-PKPEEGSGSWKNLHN
          PF.GPQN.PL.TG...EY.....I..K.....V..T...N..P..V.I.QED...PKPEEG.G.W.NLHN
Retrocopy PFHGPQNSPLRTGQAEEYQQFCDIPIK--*MTVLLTESINDLPW<VII-QEDNT<PKPEEGCGTWENLHN

Parental  FRRAELGSPTSQEGSLGESSSQDVPMEVETQFLPRTDQASPKPALTNQSSDGTSRCGINQERVHSPPKSY
          .RRAELGS..SQ.GSLG..SSQDV.MEVE.QFLPR.D.A..KP..TNQS.DG..RCGINQE.VHS.PKS.
Retrocopy SRRAELGSSISQKGSLG-*SSQDVLMEVEPQFLPRIDLAISKPFPTNQSNDGIYRCGINQESVHSYPKSH

Parental  KCEDCPRIFRF-PSQLEAHQRRHRNERPFV
          K.E.CPRI.R..P.QL..HQRRH.N.R.FV
Retrocopy KYENCPRILRY<PAQLDTHQRRHKNVRSFV

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	0.19 RPM	0.00 RPM
SRP012922_cerebellum	0.14 RPM	0.14 RPM
SRP012922_heart	0.23 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.31 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.11 RPM	0.00 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_2666 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666 , retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,