RetrogeneDB ID: retro_dnov_723

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_10173:2255..3119(-)
• 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_723
CATTTTAAATCCAGCTTCATACAACCCTCTGCTGCCACCACTACCAGGACTCAGTCTGTGTGCCAGCACCCCCCTGCTGA
CAACTGTGCCACCATGGAGGACATGAAGGAGTACAAGCAACACAGAGGAATTCACAGGGGGATCCAAGATCAATGTGAGC
AAGAACCAGCAAGATGACAGTAAAATGTTCATTGGAGGTTTGAACTGGTATACAAGCAAGAAGATCTGACTATCTCTCCA
TTTGGAGAGGTTATAGACTGTACAATTATTACAAAACTAGTCACTGGAAGATCAAGAGGCCTTGGATTTGTGCTTTTCAA
GATGTCTCTGGTGTTGATAAGGTTTTTGGAACTGAAAGAACACAAACTGGATGGCAAATTGATAAACTCCAAAAGGACAA
TAGCATTAAAAGGGAAAGAACCCCCCCAAAAAGACTTTGTGGGTGGTTTGAGCCCAGATACTTCTGAAGAACAAGTAAAA
GAATATTTTGGAACATTTGCAGAGATTGAAAACATTTAACTTCCTATGGATACAAAAACAAATGAAAGAAGAGGATTTTG
TTTTATCATTATACAAATGAAGAAACAGTAGAGAAATTATTAGAGAGCATATATCACCAGATTGGTTCTGGGAAGTGTGA
AACCAAAGTTACACAACCCAAAGCAGCAACAGCAATAACAGAAAGGAAGAAGAGGGGCTACAGCTGATGGATGAAGTGGT
ACTAGGGGCTGTGGATGAGGTCAGGGCCAAAACTGGTACCAAGGATTTAATAACTATGATGATCAAGGATAAGGGAATTA
CAATAGTGATTTATAGCTACACTATAGTGGCTATGACAGATATGATTATACTAGGTATAACTAT

Alignment

ORF - retro_dnov_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.76 %
• Parental protein coverage: 73.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  HFKSSSIQRSAAAATGTRSARQHPPADSSATMEDMNEY-SNIEEFAEGSKINASKNQQDDGKMFIGGLSW
          HFKSS.IQ.SAA..T.T.S..QHPPAD..ATMEDM.EY.SN.EEF..GSKIN.SKNQQDD.KMFIGGL.W
Retrocopy HFKSSFIQPSAATTTRTQSVCQHPPADNCATMEDMKEY>SNTEEFTGGSKINVSKNQQDDSKMFIGGLNW

Parental  DTSKK-DLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFK-DAASVDKV-LELKEHKLDGKLIDPKRAK
          .TSKK.DLT...S.FGEV.DCTI.T..VTGRSRG.GFVLFK.D...VDKV.LELKEHKLDGKLI..KR..
Retrocopy YTSKK<DLT--ISPFGEVIDCTIITKLVTGRSRGLGFVLFK<DVSGVDKV>LELKEHKLDGKLINSKRTI

Parental  ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFIT-YTDEEPVKKLLES
          ALKGKEPP.K.FVGGLSPDTSEEQ.KEYFG.F.EIENI.LPMDTKTNERRGFCFI..YT.EE.V.KLLES
Retrocopy ALKGKEPPQKDFVGGLSPDTSEEQVKEYFGTFAEIENI*LPMDTKTNERRGFCFII<YTNEETVEKLLES

Parental  RYHQIGS-GKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYN
          .YHQIGS.G....K...P.....QQQQ.QKG.RGA.A.G..GTRG.G.GQGQNW.QGFNNY.DQG.GNYN
Retrocopy IYHQIGS>GSVKPKLHNP----KQQQQ*QKGRRGATADG*SGTRGCG*GQGQNWYQGFNNYDDQG*GNYN

Parental  ST----YGGDQNYSGYGGYDY
          S.....Y.G...Y..Y..Y.Y
Retrocopy SDL*LHYSGYDRYD-YTRYNY

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	0.39 RPM	179.88 RPM
SRP012922_cerebellum	0.14 RPM	209.91 RPM
SRP012922_heart	0.00 RPM	63.58 RPM
SRP012922_kidney	0.00 RPM	105.41 RPM
SRP012922_liver	0.00 RPM	74.15 RPM
SRP012922_lung	0.00 RPM	201.14 RPM
SRP012922_quadricep_muscle	0.00 RPM	83.77 RPM
SRP012922_spleen	0.00 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_723 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,