RetrogeneDB ID: retro_dnov_2524

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8266:24321..25124(+)
• 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_2524
GATCGGATGGGAAGATGGTTTGTTGATGGAGGAGCTGCTGTTGGTCTTGGATCATTGTGCTACTATGGCCTGGGAATGTC
TAACGAGATTGGAGCCATTGAAAAGGCTGTAATTTGGCCTCAAGACGGGAAGGATAGAATTCATTCCACTTATATGTACT
TAGCAGGAAGATATGACTTCACAGCTTTGTCTGCCTTGGTAATGACCAGATCTCCTGCTCTTATGAGCTTCATGATCAGA
GGCTCTTGGGTGACGATTGGGGCCACGTTTGCAGCAATGATTGGAGCAGGCATGCTGGTGTGGTCCATCCCCTACGACCA
GAGCTGTGGCCCGAAGCACCTGACCTGGCTGCTGCATTCCGGTGTCATGGGTGCCGTGGTGGCCCCCCTGGCCATCTTGG
GGGGCCCTCTCCTCATCAGAGCTGCTTGGTACACAGCCAGCATTGTGGGCGGCCTCTCCACCGTGGCCATGTGCCGCCCA
GCGAGAAGTTCATGAACATGGGCGCCCCGCTGGGAGTGGGCCTGGGCCTCGTCTTCGTATCCTCACTGGGGTCTATGTTT
CTTCCGCCTACCACAGTGGTGGGCGCCACTCTGTACTTGGTGGCCGTCTATGGCGGATTGGTTCTTTTCAGCATGTTTCT
GCTCTTCTATACCCAGAAAGTGATCCGGCGAGCCGAAGGGGCACCACTGTACAGAGTTCAGAAGTGCGACCCCATCAGCT
CGATGATGGGAATCTACATGGATACATTAAATATATTTATACGAGTGGCCACTATGCTAGCAGGTGGAAGCAATAGAAAG
AAA

Alignment

ORF - retro_dnov_2524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 77.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DQMGRWFVAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTALSALAMTR
          D.MGRWFV.GGAAVGLG.LCYYGLGMSNEIGAIEKAVIWPQ..KDRIHSTYMYLAG....TALSAL.MTR
Retrocopy DRMGRWFVDGGAAVGLGSLCYYGLGMSNEIGAIEKAVIWPQDGKDRIHSTYMYLAGRYDFTALSALVMTR

Parental  SPALMGFMMRGSWVTIGATFAAMIGAGMLVRSIPYDQSPGPKHLAWLLHSGVMGAVVAPLAILGGPLLIR
          SPALM.FM.RGSWVTIGATFAAMIGAGMLV.SIPYDQS.GPKHL.WLLHSGVMGAVVAPLAILGGPLLIR
Retrocopy SPALMSFMIRGSWVTIGATFAAMIGAGMLVWSIPYDQSCGPKHLTWLLHSGVMGAVVAPLAILGGPLLIR

Parental  AAWYTAGIVGGLSTVAMC-APSEKFMNMGAPLGVGLGLVFVSSLGSMFLPPTTVAGATLYSVAVYGGLVL
          AAWYTA.IVGGLSTVAMC..PSEKFMNMGAPLGVGLGLVFVSSLGSMFLPPTTV.GATLY.VAVYGGLVL
Retrocopy AAWYTASIVGGLSTVAMC<PPSEKFMNMGAPLGVGLGLVFVSSLGSMFLPPTTVVGATLYLVAVYGGLVL

Parental  FSMFLLYDTQKVIWRAEGAPLYGVQKYDPINT--GIYIDALNLFM-VAAMLATGSNRKK
          FSMFLL..TQKVI.RAEGAPLY.VQK.DPI....GIY.D.LN.F..VA.MLA.GSNRKK
Retrocopy FSMFLLFYTQKVIRRAEGAPLYRVQKCDPISSMMGIYMDTLNIFIRVATMLAGGSNRKK

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	21.39 RPM	148.18 RPM
SRP012922_cerebellum	19.38 RPM	145.30 RPM
SRP012922_heart	14.39 RPM	71.23 RPM
SRP012922_kidney	29.02 RPM	130.87 RPM
SRP012922_liver	10.99 RPM	73.38 RPM
SRP012922_lung	8.71 RPM	61.85 RPM
SRP012922_quadricep_muscle	17.83 RPM	97.79 RPM
SRP012922_spleen	9.96 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_2524 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,