RetrogeneDB ID: retro_dnov_982

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_12969:16040..16988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSDNOG00000000882
• Aliases: None
• Description: polypyrimidine tract binding protein 1 [Source:HGNC Symbol;Acc:9583]

Sequence

>retro_dnov_982
TCGCTGGACGGGCAGAACATCTACAACGCCTGCTGCACGCTGCACATTGACTTCTCCAAGCTCACCAGCCTCAACGTCAA
GTACAACGACAAGAGCCGGGACTACACACGCCCTGACCTGCCCTCCGGAGACAGCCAGCCCTCGCTGGACCAGACCATGG
CCGCCGCCTTCGGTGCACCTGGCATAATCTCAGCCTCCCCGTACGCAGGAGCTGGCTTCCCTCCCACCTTTGCCCTTCCT
CAAGCTGCAGGCCTCTCTGTGCCCGACGTCCACGGAGCGCTGGCCCCTCTGGCCCTCTGCTCGGCGGCGGCGGCAGCAGC
AGCGGGCCGGATCGCCATCCCCGGCCTGGCGGGGGCGGGGAATTCGGTCTTGCTGGTTAGCAACCTGCACCCTAAGAGAG
TCACACCCCAAAGCCTCTTTATTCTTTTAGGCGTCTACGGCGACATGCAGCGGGTGAAGATGTTGTTCAACAAGAAGGAG
AATGCCCTGGGTGCAGATGGCGGACGGCAGCCAGGCGCAGCTGGCCATGAGCCACCTCAACGGGCACAAGCTGCACGGGA
AGCCGCTGCGCATCACGCTGTCCAAGCACCAGAGCGGGCAGCTGCCCCGCCAGGGCCAGGAGGACCAGGGGCTCACCAAG
GACTACGGCAGCTCGCCCCTGCACCGCTTCAAGAAGCCGGGCTCCAAGAACTTCCAGAACATCTTCCCGCCCTCCGCCAC
CCTGCACCTATCCAACGTGCCGCCTTCGGTGTCTGAGGAGGACCTCAAGATGCTCCTCTCCAGCAACGGGGGCATTGTCA
AGGGCTTCAAGTTTTTCCAGAAGGACCGCAAGAGGCGCTGATCCAGATGGGCTCGGTGGAGGAGGCCATCCGGGCGCTCA
TCGACCTGCACAACCACGACCTGGGCGAGAGCCACCACCTGCGCGTCTCCTTCTCCAAGTCCACCATC

Alignment

ORF - retro_dnov_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 58.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLDGQNISNACGKL-IDFSNLTSL--KNNDKNRNYTHPDLPCGDRQPSLDQTVASAFGAPGITSASPHAG
          SLDGQNI.NAC..L.IDFS.LTSL..K.NDK.R.YT.PDLP.GD.QPSLDQT.A.AFGAPGI.SASP.AG
Retrocopy SLDGQNIYNACCTLHIDFSKLTSLNVKYNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGAPGIISASPYAG

Parental  AGFPPTFA-PQAAGLSVPSIHGARALLALL--VAAAAAGQIAI--LAGAGNPVLLISNLHP-RVTPQSLF
          AGFPPTFA.PQAAGLSVP..HGA.A.LAL....AAAAAG.IAI..LAGAGN.VLL.SNLHP.RVTPQSLF
Retrocopy AGFPPTFALPQAAGLSVPDVHGALAPLALCSAAAAAAAGRIAIPGLAGAGNSVLLVSNLHPKRVTPQSLF

Parental  ILFGVYGDVQRVKVLFNKKENAL-VQMADGSQAQLAMSHLNGHKLHGKPLRITLSKHQSVQLPREGQEDG
          IL.GVYGD.QRVK.LFNKKENAL.VQMADGSQAQLAMSHLNGHKLHGKPLRITLSKHQS.QLPR.GQED.
Retrocopy ILLGVYGDMQRVKMLFNKKENAL>VQMADGSQAQLAMSHLNGHKLHGKPLRITLSKHQSGQLPRQGQEDQ

Parental  KPPKNSGSSPLHRFKKPGSKNFQNIFPPSATLHLSNVPPSVSEEDLKMLFSSNGGIVKGFKFFQKDRKM-
          ...K..GSSPLHRFKKPGSKNFQNIFPPSATLHLSNVPPSVSEEDLKML.SSNGGIVKGFKFFQKDRK..
Retrocopy GLTKDYGSSPLHRFKKPGSKNFQNIFPPSATLHLSNVPPSVSEEDLKMLLSSNGGIVKGFKFFQKDRKR<

Parental  ALIQMGSVEEAIQALIDLHNHDLGESHHLRVSFSKSTI
          ALIQMGSVEEAI.ALIDLHNHDLGESHHLRVSFSKSTI
Retrocopy ALIQMGSVEEAIRALIDLHNHDLGESHHLRVSFSKSTI

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	98.98 RPM	128.15 RPM
SRP012922_cerebellum	18.15 RPM	32.44 RPM
SRP012922_heart	7.19 RPM	10.44 RPM
SRP012922_kidney	32.31 RPM	38.06 RPM
SRP012922_liver	29.57 RPM	41.02 RPM
SRP012922_lung	65.67 RPM	90.11 RPM
SRP012922_quadricep_muscle	6.58 RPM	7.62 RPM
SRP012922_spleen	85.73 RPM	116.06 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_982 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982 ,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,