RetrogeneDB ID: retro_dnov_1990

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_40679:6062..6929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSDNOG00000013226
• Aliases: None
• Description: heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]

Sequence

>retro_dnov_1990
ATGCTTCGATTACCCGCAGTCCTTCGCCAGATGAGGCCAGTGTCCAGGGCATTGGCTCCTCATCTCATTCGGGCATATGC
CAAAGATGTGAAATTCGGTGCCGATGCCCGAGCCTTAATGCTTCAAGGTGTAGACCTTTTAGCTGATGCTGTAGCCGTTA
CTATGGGGCCAAAGGGAAGAACAGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACCGTT
GCAAAATCAATTGATTTGAAGGATAAATATAAAAATATTGGAGCTAAGCTTGTTCAGGATGTTGCCAATAACACAAATGA
AGAGGCTGGGGATGGCACCACCACTGCTACTGTACTGGCACGCTCTATTGCTAAGGAAGGCTTTGAGAAGATTAGCAAAG
GTGCTAATCCAGTAGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTAATTGCTGAACTTAAGAAGCAGTCTAAA
CCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGAAATTGGCAATATCATTTC
TGATGCAATGAAAAAGGTTGGAAGAAAAGGTGTCATCACAGTAAAGGATGGAAAAACATTGAATGATGAATTAGAAATCA
TTGAAGGCATGAAGTTTGATCGGGGTTATATTTCTCCATATTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAG
GATGCCTATGTTCTGTTAAGTGAAAAGAAAATTTCTAGCATTCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTCA
CCGTAAGCCCTTGGTCATAATTGCTGAAGATGTTGATGGAGAAGCTCTAAGTACACTTGTTTTGAAT

Alignment

ORF - retro_dnov_1990 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRLPAVLRQMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
          MLRLPAVLRQMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
Retrocopy MLRLPAVLRQMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS

Parental  PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
          PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
Retrocopy PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI

Parental  RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
          RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
Retrocopy RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE

Parental  LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVTALEIANAYRKPLVIIAEDVDG
          LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIV.ALEIANA.RKPLVIIAEDVDG
Retrocopy LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVPALEIANAHRKPLVIIAEDVDG

Parental  EALSTLVLN
          EALSTLVLN
Retrocopy EALSTLVLN

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	83.04 RPM	108.32 RPM
SRP012922_cerebellum	21.86 RPM	29.56 RPM
SRP012922_heart	33.64 RPM	46.41 RPM
SRP012922_kidney	78.85 RPM	138.54 RPM
SRP012922_liver	62.39 RPM	97.22 RPM
SRP012922_lung	30.24 RPM	48.57 RPM
SRP012922_quadricep_muscle	43.96 RPM	49.68 RPM
SRP012922_spleen	44.41 RPM	59.63 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_1990 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 16 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Bos taurus	ENSBTAG00000012586	1 retrocopy	retro_btau_988,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus	ENSDNOG00000013226	3 retrocopies	retro_dnov_1990 , retro_dnov_2113, retro_dnov_2512,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Tursiops truncatus	ENSTTRG00000003417	3 retrocopies	retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,