RetrogeneDB ID: retro_dnov_1466

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_208942:32..647(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSDNOG00000016588
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_dnov_1466
AGAGGAGTTACGACAACACAGGGTTCATTTCCCAAAACATTTTATAATTTCTGGCTCATCGTTTGCCAAAAAAGACAAAA
GCAGTTATTTACTGAACTGGGTTGTGGAGAAATAATCGGTTAAATGTGCATAGTATTGGCCGAGAAAATATGCCTGAGAG
ATGCTGTTTAAAGAAACGGGATCCAGTCTGTAGCTTTTATCAGAAGACGTGAAATAACATTATACAGTACATCTACCATA
ATTAGAAAATATCAATAATGGTGAAGCCGGAACCTTATCTCACTTTCATTATACTACCTGGCCAGATTTTGGAGTCCCTG
AATCAGTAGCTTCATTTCTCAATTTCCTACTTAAAAGTGTTAGAATCTAGCTCCTTCAACTCTGAGCATGGGTCTGAAGT
AATCCCCGATAGTGCAGGAATTGGGCAATCTGGCACCTTTTCTTTAGTAGACACTTGTCTTGTTTTGATGGAAAATATGA
TATTAATATTAAACAAGTTTTGCTGAATATGAGAAAATATTGAATGACGTTACTGAAACACCAGATCAACTCAGATTCTA
ATATGTGAATATACTAGAAGGAGCAAAGTTTATAAAGGGAGATTTAAATATACAG

Alignment

ORF - retro_dnov_1466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RSYVLTQGPLPNTCCHFWLMVWQQ-KTKAVV-MLNRVVEKESVKCAQYWPTKDDREMLFKETGFSVKLLS
          R....TQG..P.T...FWL.V.Q..KTKAV...LN.VVEK.SVKCA.YWP.K...EMLFKETG.S..LLS
Retrocopy RGVTTTQGSFPKTFYNFWLIVCQK<KTKAVI<LLNWVVEK*SVKCA*YWPRKYA*EMLFKETGSSL*LLS

Parental  EDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFL-FKVRESGSLNPEHGPAVIHC
          EDVK..YTVHL..LENIN.GE..T.SHFHYTTWPDFGVPES.ASFLNFL..KV.ES.S.N.EHG..VI..
Retrocopy EDVK*HYTVHLP*LENINNGEAGTLSHFHYTTWPDFGVPESVASFLNFL>LKVLESSSFNSEHGSEVIPD

Parental  SAGIGRSGTFSLVDTCLVLME-KGDDINIKQVLLNMRKYRMGLI-QTPDQLRFSYMAILEGAKFIKGDSN
          SAGIG.SGTFSLVDTCLVLME.K.D.INIKQVLLNMRKY.M.L...TPDQLRF.Y..ILEGAKFIKGD.N
Retrocopy SAGIGQSGTFSLVDTCLVLME<KYD-INIKQVLLNMRKY*MTLL<ETPDQLRF*YVNILEGAKFIKGDLN

Parental  IQ
          IQ
Retrocopy IQ

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	17.11 RPM
SRP012922_cerebellum	0.00 RPM	17.87 RPM
SRP012922_heart	0.00 RPM	9.05 RPM
SRP012922_kidney	0.00 RPM	14.78 RPM
SRP012922_liver	0.00 RPM	9.29 RPM
SRP012922_lung	0.00 RPM	20.92 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.96 RPM
SRP012922_spleen	0.00 RPM	33.88 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_1466 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466 ,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,