RetrogeneDB ID: retro_itri_696

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:300322..301134(-)
• Located in intron of: ENSSTOG00000024054

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSSTOG00000001407
• Aliases: None
• Description: zinc finger, CCHC domain containing 9 [Source:HGNC Symbol;Acc:25424]

Sequence

>retro_itri_696
ATGACCAGGTGGGCAGAGTTACTACCACACATAAAAAGAGGCCCTTGCCTGCAACATCATGGGAGGACATGAAGAAGGGG
TCCTTGGAGGGAACAAGCCCAAATCTACCAAATCGTAAACAACCTGAAGCCAATAGACTGTCCCTTAAAAATGTTGCACC
CCAAGCAAAACATAAAAAGAACAAAAGGAAGAAAGAATACTTAAATGAAGATGTGAATGGATTCATGGAATACCTAAAAC
AGAACTCACAGATGGTTCACAATGTGGAGATGATAGCAATGGACAGCCAGGAAGTAAGGGAAGAAATTGCAGTTGCTTTA
AAGAAAGACAGTTGATGGGAAGGAAGACGATTAAAAAGACAAGCAGCGAAGAAAAACGCAAGGGTATGTTTCCACTATAG
AAAACCTGGCCAGGGAATTGCAGATTGCCCAGCTGCCCTTGTAAATCAAGATATGGGCACTGGAATATGTTATTGATGTG
GGTCCACAGAGCATGAAATAACCAAGTGCAAGGCTAAAGTAGACCCAGCTCTTGGTGAATTTCCTTTTGCAAAATGTTTT
GTTTGTGGGGAAATGGGGCATCTGTCCCATTCATGTCCTGATAATCACAAAGGATTCTATGTTGATGGTGGTGGTTGCAA
ACTTTGTAGTTTTGTGGAACACTTTAAGAAAGATTGCCTTGAAAGTCATAATTCAGATCGAATGGTCACAGTTGGTCACT
GGGCAAAGGGGATGAGTGCAGACTATGAAGAAATTTTGGATGTGCCAAAACCAAAGAAACCCAAAATAAAAATACCTAAA
GTTGTCAATTTT

Alignment

ORF - retro_itri_696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTRWA-RVTTTHNKRPLPATSWEDMKKGSLEGTSQ---NRKQPEVNRLSLKNVAPQAKHKKNKKKKEYLN
          MTRWA.RVTTTH.KRPLPATSWEDMKKGSLEGTS....NRKQPE.NRLSLKNVAPQAKHKKNK.KKEYLN
Retrocopy MTRWA<RVTTTHKKRPLPATSWEDMKKGSLEGTSPNLPNRKQPEANRLSLKNVAPQAKHKKNKRKKEYLN

Parental  EDVNGFMEYLKQNSQMVHNGEMIAMDSQEVREEIAVALKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHG
          EDVNGFMEYLKQNSQMVHN.EMIAMDSQEVREEIAVALKKDS..EGRRLKRQAAKKNA.VCFH.RKPG.G
Retrocopy EDVNGFMEYLKQNSQMVHNVEMIAMDSQEVREEIAVALKKDS*WEGRRLKRQAAKKNARVCFHYRKPGQG

Parental  VADCPAALENQDMGTGICYRCGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYAD
          .ADCPAAL.NQDMGTGICY.CGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLS.SCPDN.KG.Y.D
Retrocopy IADCPAALVNQDMGTGICY*CGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSHSCPDNHKGFYVD

Parental  GGGCKLCGSVEHFKKDCPESQNSDRMVTVGRWAKGMSADYEEILDMPKPKKSKTKIPKVVNF
          GGGCKLC..VEHFKKDC.ES.NSDRMVTVG.WAKGMSADYEEILD.PKPKK.K.KIPKVVNF
Retrocopy GGGCKLCSFVEHFKKDCLESHNSDRMVTVGHWAKGMSADYEEILDVPKPKKPKIKIPKVVNF

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_696 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_696 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 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Microcebus murinus	ENSMICG00000016266	5 retrocopies	retro_mmur_125, retro_mmur_1325, retro_mmur_1341, retro_mmur_606, retro_mmur_819,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696 ,
Tarsius syrichta	ENSTSYG00000012423	1 retrocopy	retro_tsyr_244,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,