RetrogeneDB ID: retro_dnov_708

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_100354:5678..6392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GHITM
• Ensembl ID: ENSDNOG00000018880
• Aliases: None
• Description: growth hormone inducible transmembrane protein [Source:HGNC Symbol;Acc:17281]

Sequence

>retro_dnov_708
GATGAGACAGGAAGAGGGTTTGTTGCTGGAGGAGCTGCGGTTGGTCTTGGAACATTGTGCTGCTATGGCTTGGGAATGTC
TAAAGACAGTGGTGCTCTTGAAAAGGCTGCAATCTGGCCTCATTATGTGAAGGAGAGGATTCAGTCTACCCGTATGTACT
TAGCAGGAAGGACTGATTCAATAGCTTTGTCTGCCTTGGCAGGGAGCAGAACTCCTATCTCATGAACATGATGAGAGGCT
CTTGGGTGATAGTTAATGCAACCTTTGTAGACCTGATTAGAGCTGAAATGCTGGTGCAATTGATATCCTATGACCAGAGT
CCTGGCCCAAAGCATCTTGCTTGGTTGCTGCTTTCTGGGTGATGGGTGCAGTGGTGGCTCCTCTGACGATAGTAGGAGGC
ACTCCTTTCATCAGAGCTGCTTGGTACACAGATGGCATTGTGGGCGGCCTCTCCACTGCAGCCAGGCATGCTCCCAGTGA
GAAGGTGGTGAACATGGGCACACCCCTGAGAATGGGCGAGGTCGCGTCTCTGTTCATCTCTGGGATCTGGTTCTTCCTTC
TACCACAGTGGCTGGTGCCACTCTGTACTGAGTGGCAGTTTATGGTTGATTAGTTCTTTACAGCCTATTCTTCTTATACA
ACACCCAGAAAGTAATCGGGCTTGCTGAAATAGCACTGTTACGTGGCAGTCAAAAATACGATCTCATCAATTCC

Alignment

ORF - retro_dnov_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.03 %
• Parental protein coverage: 70.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DQMGRWFVAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTALSALAMTR
          D..GR.FVAGGAAVGLG.LC.YGLGMS...GA.EKA.IWP.YVK.RI.ST.MYLAG.....ALSALA..R
Retrocopy DETGRGFVAGGAAVGLGTLCCYGLGMSKDSGALEKAAIWPHYVKERIQSTRMYLAGRTDSIALSALAGSR

Parental  SPA-LMGFMMRGSWVTIGATFAAMIGAGMLVRSIPYDQSPGPKHLAWLLHSG-VMGAVVAPLAILGGPLL
          .P..LM..MMRGSWV...ATF...I.A.MLV..I.YDQSPGPKHLAWLL.SG.VMGAVVAPL.I.GG...
Retrocopy TPI<LMN-MMRGSWVIVNATFVDLIRAEMLVQLISYDQSPGPKHLAWLLLSG<VMGAVVAPLTIVGGTPF

Parental  IRAAWYTAGIVGGLSTVAMCAPSEKFMNMGAPLGV-GLGLVFVSSLGSMFLPPTTVAGATLYSVAVYGGL
          IRAAWYT.GIVGGLST.A..APSEK..NMG.PL...G.G.V.V..L....LP.TTVAGATLY.VAVYG.L
Retrocopy IRAAWYTDGIVGGLSTAARHAPSEKVVNMGTPLRM<GRGRVSVH-LWDLVLPSTTVAGATLY*VAVYG*L

Parental  VLFSMFLLYDTQKVIWRAEGAPLYGVQKYDPINT
          VL.S.F.LY.TQKVI..AE.A.L.G.QKYD.IN.
Retrocopy VLYSLFFLYNTQKVIGLAEIALLRGSQKYDLINS

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	148.18 RPM
SRP012922_cerebellum	0.00 RPM	145.30 RPM
SRP012922_heart	0.00 RPM	71.23 RPM
SRP012922_kidney	0.27 RPM	130.87 RPM
SRP012922_liver	0.00 RPM	73.38 RPM
SRP012922_lung	0.00 RPM	61.85 RPM
SRP012922_quadricep_muscle	0.00 RPM	97.79 RPM
SRP012922_spleen	0.00 RPM	59.86 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_708 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708 , retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,