RetrogeneDB ID: retro_dnov_144

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2066:152074..152785(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000003887
• Aliases: None
• Description: None

Sequence

>retro_dnov_144
AAGCAAGAAAGATCTGACTATTTGTCTCGATTTGGAGAAGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGAAG
ATCAAGAGGATTTGGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGAGAAGGTTTTGGAACTGAAGGAACACAAACTGG
ATGGCAAATTGATAGACCCCAAAAGGGCGAAGGCATTAAAAGGGAAAGAACCCCCAAAAAAGGTCTTTGTAGGTGGTTTG
AGCCCAGATACTTCTGAAGAACAAATAAAATAATATTTTGGAGCATTCGGAGAGATTGAAAACATTGAACTTCCTATGGA
TACAAAAACAAATGAAAGAAGAGGCTTTTGTTTTATCACATATACAGATGAAGAGCCAGTAAAGAAATTATTAGAGAGCA
GATACCATCAGATTGGTTCTGGGAAGTGTGAAATCAAAGTTGCACAACCCAAAGAAGTATATAGGCAGCAACAGCAACAA
CAGAAAGGAGGGAGAGGGGCTGCAGCTGGTGGACGAGGTGGTACTAGGGGTCGTGGACGAGGTCAGGGCCCAAACTGGAA
CCAAGGATTTAATAACTATTATGATCAAGGATATGGAAATTACAATAGTACCTATGGTGGTGATCAAAACTATAGTGGCT
ATGGCGGATATGATTATACTGGGTATAACTATGGGAGCTATGGATATGGACAGGGATATGCAGACTATAGT

Alignment

ORF - retro_dnov_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.62 %
• Parental protein coverage: 59.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKE
          K.....YLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASV.KVLELKEHKLDGKLIDPKRAKALKGKE
Retrocopy KQERSDYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVEKVLELKEHKLDGKLIDPKRAKALKGKE

Parental  PPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGS
          PPKKVFVGGLSPDTSEEQIK.YFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGS
Retrocopy PPKKVFVGGLSPDTSEEQIK*YFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGS

Parental  GKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSTYGGDQN
          GKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQG.NWNQGFNNYYDQGYGNYNSTYGGDQN
Retrocopy GKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGPNWNQGFNNYYDQGYGNYNSTYGGDQN

Parental  YSGYGGYDYTGYNYGSYGYGQGYADYS
          YSGYGGYDYTGYNYGSYGYGQGYADYS
Retrocopy YSGYGGYDYTGYNYGSYGYGQGYADYS

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	4.47 RPM	179.88 RPM
SRP012922_cerebellum	7.84 RPM	209.91 RPM
SRP012922_heart	2.78 RPM	63.58 RPM
SRP012922_kidney	4.38 RPM	105.41 RPM
SRP012922_liver	2.01 RPM	74.15 RPM
SRP012922_lung	8.25 RPM	201.14 RPM
SRP012922_quadricep_muscle	3.46 RPM	83.77 RPM
SRP012922_spleen	5.72 RPM	176.61 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_144 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 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144 , retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,