RetrogeneDB ID: retro_itri_1539

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393533.1:769653..770188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CACYBP
• Ensembl ID: ENSSTOG00000010859
• Aliases: None
• Description: calcyclin binding protein [Source:HGNC Symbol;Acc:30423]

Sequence

>retro_itri_1539
CGGAAGAAACCAGAACTTCTTGGCAATGAAAAGCCAGCTGCTGTGTGTGCTCCCATCACAACAGGATATACCATGAAAAT
CAGTAATTATAGATGGGATCAATCCGATACGTTTTTGAAAATCTACATCACTTTAATGGGAGTTCATCAAGTTACCACCC
AGAATGTGCAGGTTCATTTCACAGAGAGGTCATTTGATCTTTTGGTAAAGAATCTAAATGGGAAGAGTTACTCCATGATT
ATGAATCTCTTGAAACCCATGTCTGCGGAAGGCAGTTCAAAAAAAGTTAAGACTGATACAGTTCTCATCTTATGTAGGAA
GAAAGCAGAAAACACACGGTGGGGGTATTTGACTAAGGTTGCAAAAGAATGCAAAGAGAGAAAAGCCTTCAGAAGCCACC
GAAACAGATCCTAGTGAGGGATTAATGAATGTTCTAAAGAAAATTTATAAAGATGGAGATGATGTTATGAAGTGAGCCAT
TAATACAGACTGAGTAGAATCAAGAGAGAAGCAAGCCAAAGAAGATACAGAATTT

Alignment

ORF - retro_itri_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 80.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKKPELLDNEKPAAVVAPITTGYTVKISNYGWDQSDKFVKIYITLTGVHQVPAENVQVHFTERSFDLLVK
          .KKPELL.NEKPAAV.APITTGYT.KISNY.WDQSD.F.KIYITL.GVHQV...NVQVHFTERSFDLLVK
Retrocopy RKKPELLGNEKPAAVCAPITTGYTMKISNYRWDQSDTFLKIYITLMGVHQVTTQNVQVHFTERSFDLLVK

Parental  NLNGKSYSMIVNNLLKPISVEGSSKKVKTDTVLILCRKKAENTRWEYLTQV-EKECKEKEKPSYDTETDP
          NLNGKSYSMI.N.LLKP.S.EGSSKKVKTDTVLILCRKKAENTRW.YLT.V..K..K..EKPS..TETDP
Retrocopy NLNGKSYSMIMN-LLKPMSAEGSSKKVKTDTVLILCRKKAENTRWGYLTKV>QKNAK-REKPSEATETDP

Parental  SEGLMNVLKKIYEDGDDDMKRTINKAWVESREKQAKGDTEF
          SEGLMNVLKKIY.DGDD.MK..IN...VESREKQAK.DTEF
Retrocopy SEGLMNVLKKIYKDGDDVMK*AINTD*VESREKQAKEDTEF

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_1539 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1539 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 26 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000170	4 retrocopies	retro_amel_1094, retro_amel_1760, retro_amel_571, retro_amel_975,
Bos taurus	ENSBTAG00000001107	1 retrocopy	retro_btau_1122,
Canis familiaris	ENSCAFG00000029016	1 retrocopy	retro_cfam_1724,
Callithrix jacchus	ENSCJAG00000008989	4 retrocopies	retro_cjac_2432, retro_cjac_3336, retro_cjac_964, retro_cjac_975,
Cavia porcellus	ENSCPOG00000012682	7 retrocopies	retro_cpor_1057, retro_cpor_1207, retro_cpor_1208, retro_cpor_1276, retro_cpor_1462, retro_cpor_581, retro_cpor_759,
Dasypus novemcinctus	ENSDNOG00000015629	1 retrocopy	retro_dnov_915,
Dipodomys ordii	ENSDORG00000001870	1 retrocopy	retro_dord_490,
Erinaceus europaeus	ENSEEUG00000014973	2 retrocopies	retro_eeur_431, retro_eeur_507,
Echinops telfairi	ENSETEG00000009331	3 retrocopies	retro_etel_192, retro_etel_1921, retro_etel_766,
Felis catus	ENSFCAG00000008591	3 retrocopies	retro_fcat_539, retro_fcat_875, retro_fcat_954,
Homo sapiens	ENSG00000116161	2 retrocopies	retro_hsap_2355, retro_hsap_706,
Gorilla gorilla	ENSGGOG00000005962	2 retrocopies	retro_ggor_1788, retro_ggor_601,
Macropus eugenii	ENSMEUG00000010725	5 retrocopies	retro_meug_1472, retro_meug_1517, retro_meug_1751, retro_meug_236, retro_meug_95,
Macaca mulatta	ENSMMUG00000001571	1 retrocopy	retro_mmul_175,
Mustela putorius furo	ENSMPUG00000004813	3 retrocopies	retro_mputfur_1058, retro_mputfur_1122, retro_mputfur_859,
Mus musculus	ENSMUSG00000014226	4 retrocopies	retro_mmus_1443, retro_mmus_2019, retro_mmus_2051, retro_mmus_567,
Nomascus leucogenys	ENSNLEG00000015357	3 retrocopies	retro_nleu_126, retro_nleu_2513, retro_nleu_318,
Oryctolagus cuniculus	ENSOCUG00000004358	3 retrocopies	retro_ocun_1249, retro_ocun_1362, retro_ocun_1852,
Otolemur garnettii	ENSOGAG00000005375	2 retrocopies	retro_ogar_2507, retro_ogar_2720,
Ochotona princeps	ENSOPRG00000000316	1 retrocopy	retro_opri_674,
Procavia capensis	ENSPCAG00000003742	3 retrocopies	retro_pcap_237, retro_pcap_300, retro_pcap_449,
Pongo abelii	ENSPPYG00000000486	3 retrocopies	retro_pabe_207, retro_pabe_2130, retro_pabe_520,
Pan troglodytes	ENSPTRG00000001705	2 retrocopies	retro_ptro_1723, retro_ptro_505,
Rattus norvegicus	ENSRNOG00000002572	2 retrocopies	retro_rnor_2734, retro_rnor_589,
Ictidomys tridecemlineatus	ENSSTOG00000010859	4 retrocopies	retro_itri_1539 , retro_itri_732, retro_itri_807, retro_itri_808,
Tursiops truncatus	ENSTTRG00000010399	1 retrocopy	retro_ttru_682,