RetrogeneDB ID: retro_itri_1561

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393541.1:277338..277769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSSTOG00000024828
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 2 [Source:HGNC Symbol;Acc:1490]

Sequence

>retro_itri_1561
GTTTATGCTAAAACTATAGATTGTCAGCAGACTATTATTGCATGTATTAAAAGCCACCAGTTTCACCCTAAAAACTTTTG
GCATGGCCACTGGAAATCAGAGTGGAAGTTCACTAACACAATACCTACAGCCCAGGTGGTTGGAGTGCTCAAGATTCACC
TTCACAATTATGAAGATAGAACATTCAGATGGTGAGTCATAAAGATATATGAGATTCAATAACTGTTTTGAATGAGGTCC
AAACTGCCAAGGAGTTTATTAACATCATAGAGAGTGCAGAAAATGAATATCAGACAGCAATTAGTGAAAACTATCAAACA
ATATCAGATACCACATTCAAGGCCTGGAGCCAGCAGCTTCCAGTTACCCACACCAAAATTGACTGGAACAAGATCCTCAG
CTACAAGATTGGCCAAGAAATGCAGAATGCT

Alignment

ORF - retro_itri_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 50.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VYGKKIDGQQTIIACIESHQFQAKNFWNGRWRSEWKFTITPSSTTQVVGILKIQVHYYEDG-NVQLVSHK
          VY.K.ID.QQTIIACI.SHQF..KNFW.G.W.SEWKFT.T...T.QVVG.LKI..H.YED..N.Q.VSHK
Retrocopy VYAKTIDCQQTIIACIKSHQFHPKNFWHGHWKSEWKFTNT-IPTAQVVGVLKIHLHNYEDR<NIQMVSHK

Parental  DIQDYLTVSSEMQTAKEFIKIVEAAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIG
          DI.D..TV..E.QTAKEFI.I.E.AENEYQTAISENYQT.SDTTFKA...QLPVT.TKIDWNKILSYKIG
Retrocopy DI*DSITVLNEVQTAKEFINIIESAENEYQTAISENYQTISDTTFKAWSQQLPVTHTKIDWNKILSYKIG

Parental  KEMQNA
          .EMQNA
Retrocopy QEMQNA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1561 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561 ,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,