RetrogeneDB ID: retro_dnov_815

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_10989:78196..79120(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSDNOG00000012883
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_dnov_815
GCCAGCATGAGCTCCTCGCAGTTCAACAAGGGCCCCTCGTACGGGCTCTCGGCCGAGGTCAAGAACCGGCTCCTGTCCAA
ATATGACCCTCAGAAGGAGGCAGAGCTCCGCAGCTGGATCGAGGGGCTCACGGGACTTTCTATTGGCCCCGACTTCCAGA
AAGGCCTGAAGGATGGAGTTATCTTGTGCACGCTCATGAACAAGCTGCAGCCGGGCTCCGTCCCCAAGGTCAACCGCTCC
CAGCAGAACTGGCACCAGCTGGAGAACCTGTCCAACTTCATCAAGGCCATGGTCGGCTACGGCATGAACCCCGTGGACCT
GTTCGAAGCCAACGACCTCTTCGAGAGCGGGAACCTGACGCAGGTGCAGGTGTCCCTCCTCGCCCTGGCCGGGAAGGCCA
AGACGAAGGGGCTGCAGAGCGGCGTGGACATCGGCGTCAAGTACTCTGAGAAGCAAGAGCGCAACTTCGACGACGCCACC
ATGAAGGCGGGCCAGTGCGTCATCGGGCTGCAGATGGGCACTAACAAGTGCGCCAGCCAGTCGGGCATGACGGCGTATGG
CACGCGGCGGCACCTGTACGACCCCAAGAACCACATCCTGCCGCCCATGGACCACTCCACCATCAGTCTCCAGATGGGCA
CCAACAAGTGTGCCAGCCAGGTGGGCATGACGGCTCCGGGGACCCGGCGGCACATTTACGACACCAAGCTGGGCACCGAC
AAGTGCGACAACTCTTCCATGTTCCTGCAGATGGGCTACGCGCAGGGAGCCAACCAGAGCGGCCAGGTCTTTGGCCTGGG
CCGCCAGATCTATGACCCCAAGTACTGCCCACAGGGCCCGGGGGCCGATGGGGCGCCCTCAGGCGCCGGCGACTGCCCGG
ACGCCCCCGAGGCCCCCGAGTATGCTCCCTACTACCAGGAGGAG

Alignment

ORF - retro_dnov_815 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.13 %
• Parental protein coverage: 77.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARATMTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRSWIEEVTGMSIGTNFQLGLKDGIILCELINKLQ
          A......FNKGPSYGLSAEVKN...SKYD.Q.E..LRSWIE..TG.SIG..FQ.GLKDG.ILC.L.NKLQ
Retrocopy ASMSSSQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQ

Parental  PGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHT
          PGSV.KVN.S..NW.QLEN..NFIKA...YGM.P.D.FEANDLFE.GN.TQVQ..L.ALAG.AKTKG...
Retrocopy PGSVPKVNRSQQNWHQLENLSNFIKAMVGYGMNPVDLFEANDLFESGNLTQVQVSLLALAGKAKTKGLQS

Parental  -IDIG-EYAEKQ-RRFDXXXXXXXXXXXXXXMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISL
          ..DIG..Y.EKQ.R.FD..............MGTNKCASQ.GMTAYGTRRHLYDPK.....P.D..TISL
Retrocopy GVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL

Parental  QMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAP
          QMGTNK.ASQ.GM.APGTRR.IYD.KL.....DNS...LQMG....A.Q.G..V.GLGRQ.YDPKYC..P
Retrocopy QMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMFLQMGYAQGANQSG-QVFGLGRQIYDPKYC--P

Parental  TEPVIHNGSQGTGTNGSEISDSDYQAEYPDE
          ..P.......G.G..........Y...Y..E
Retrocopy QGPGADGAPSGAGDCPDAPEAPEYAPYYQEE

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	38.12 RPM	140.99 RPM
SRP012922_cerebellum	7.01 RPM	78.22 RPM
SRP012922_heart	16.47 RPM	30.16 RPM
SRP012922_kidney	25.46 RPM	133.06 RPM
SRP012922_liver	18.89 RPM	72.45 RPM
SRP012922_lung	134.70 RPM	197.47 RPM
SRP012922_quadricep_muscle	4.67 RPM	22.67 RPM
SRP012922_spleen	226.29 RPM	171.23 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_815 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus	ENSDNOG00000012883	3 retrocopies	retro_dnov_223, retro_dnov_403, retro_dnov_815 ,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,