RetrogeneDB ID: retro_dnov_2498

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_80521:4394..4936(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSDNOG00000005210
• Aliases: None
• Description: cyclin G2 [Source:HGNC Symbol;Acc:1593]

Sequence

>retro_dnov_2498
GTGAAACCTAAAATTTGTCTTGCACTGGAGTCTGTTGTTTTACTGGCTGCCAGAATAGTTGAAGAAGAATGCAATGTTCC
ATCCACTTGCGAAATAATCCAGATTAGTCAATGTAAATGCACTGCTTCTGACAGAAAATGAGGGGAAAAATAATTTAAGA
AAACAATTCAAAACTATGAATTGGAAGCTACTACCATTTTAAACTTTTTCTCCTATATAAAACAACTGTACTTCTTCATA
CTTCAGAAAGGAAAGATAATATTGAGCCTTGATAAACTGGAAGCTCAGCCAAAAGCTTGCAATTTCCTACTAGTCTTTTC
AAAAGCGAAACCATCTGTATTAGCTTTGTGCTTTCTCAATCTGGAAGTAGAAACCTTGTAATTCATTAAATTATTGCAAA
TTCTCCTGCTTGTTAAAAGCATTCAAAAGTTTAACAAAACCAAGATCTCATACTGGAGGGAGGTAGTTTCCAAATACCTC
GCTGAGTATTTTCTCTTGAATGCTGTAATTTGGATCACAGTAAGTTGGTTTGAACTGTTTCA

Alignment

ORF - retro_dnov_2498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.38 %
• Parental protein coverage: 85.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VKPK-HLSCIGVCC-FLLAARIVEEECNIPLTHDVIRISQCKCTASDIKRMEKIISEKL-HYELEATTAL
          VKPK..LSC.GV.C..LLAARIVEEECN.P.T...I.ISQCKCTASD.K..EK........YELEATT.L
Retrocopy VKPK<NLSCTGV-C>VLLAARIVEEECNVPSTCEIIQISQCKCTASDRK*GEK*FKKTIQNYELEATTIL

Parental  NFLH-LYHSIVFCHTSERKE-ILSLDKLEAQLKACNCRLVFSKAKPSVLALCLLNLEVETLKSMELLEIL
          NF...LY...V..HTSERK..ILSLDKLEAQ.KACN..LVFSKAKPSVLALC.LNLEVETL....LL.IL
Retrocopy NFFS<LYKTTVLLHTSERKD>ILSLDKLEAQPKACNFLLVFSKAKPSVLALCFLNLEVETL*FIKLLQIL

Parental  LLVKKHSKVNDTEFFYWRELVSKCLAEY-SSPECCKPDHKKLVWIVS
          LLVK...K.N.T...YWRE.VSK.LAEY..S.ECC..DH.KLV..VS
Retrocopy LLVKSIQKFNKTKISYWREVVSKYLAEY<FSLECCNLDHSKLV*TVS

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	13.22 RPM
SRP012922_cerebellum	0.00 RPM	24.19 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.00 RPM	5.20 RPM
SRP012922_liver	0.00 RPM	3.25 RPM
SRP012922_lung	0.00 RPM	18.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	19.92 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_2498 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013793	1 retrocopy	retro_amel_960,
Dasypus novemcinctus	ENSDNOG00000001502	1 retrocopy	retro_dnov_2629,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498 ,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Felis catus	ENSFCAG00000026008	1 retrocopy	retro_fcat_1062,
Macropus eugenii	ENSMEUG00000008707	1 retrocopy	retro_meug_1962,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358,
Nomascus leucogenys	ENSNLEG00000008169	1 retrocopy	retro_nleu_933,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pan troglodytes	ENSPTRG00000016196	1 retrocopy	retro_ptro_773,
Sus scrofa	ENSSSCG00000008988	1 retrocopy	retro_sscr_813,
Ictidomys tridecemlineatus	ENSSTOG00000027922	1 retrocopy	retro_itri_1112,
Tupaia belangeri	ENSTBEG00000007671	2 retrocopies	retro_tbel_2258, retro_tbel_38,
Tursiops truncatus	ENSTTRG00000014837	1 retrocopy	retro_ttru_491,