RetrogeneDB ID: retro_itri_369

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:11408145..11409143(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA7
• Ensembl ID: ENSSTOG00000009026
• Aliases: None
• Description: cell division cycle associated 7 [Source:HGNC Symbol;Acc:14628]

Sequence

>retro_itri_369
GCAAACCAGGAAGGCTGTAAGACCCGCAGCCAGGATAGGACCCGCAGCCAGTACAGACTTTCTGGACCTCTCAGGGTGGC
GATGAAGTTCCCAGCAGGAAACACCAGGAGTGCAGCCAACAAAAAAGTAGCACCCCCCAAGCCCTCAGAAAATTTCACTA
CTGACTCCGATTCTGATTCAGAAGATGAAAGTGGCATGAACTTTCTTGAGAAAAGGGCTTTACATATATAAAGCAGAACA
AAGCAATGTTTGCAAAACTCATGTCAGAATTAGAAAGCTTCCCTGGTTCCTTTCCTGGAAGATGTTCCCTCCCAGGCCCA
AGATCAGTAAATGAGTCAAAGACACCCTGAAGGCGTACATTCCCAGGTGTGGCTTCCAGGAGGAACCCTGACCCGGAGAG
CTCTGACTGGAGTCCTCTGTCTAGGTCAAGGTCCCGGATCTTGGGGTCCCTTAGTGCTCTTCCCACAGAAGAGGAGGAGG
AAGAAGAGGAAGATGATAAGTTTATGCTGGTGAGAAAGAGGAAAACTGTGGACAGATACATGAACGATGATGATAGGCCC
AGAAGTCGGCGCCCAGGATCCATGACCCTTCCGCAAATAATTCGCCCAGGGGAAGAAATCACAGAGGATGAGTTGGGGAA
CATCTGCAGCAACTCTCGAGAGAAGATATAGAACCGTTCACTGGGACCTACTTGTCATCAGTGCGGACAGAAAACCATTG
ATACCAAAACAAACTGCAGAAACCTAGGCTGCTGGGGCACTCAAGGCCAGTTCTGTGGTCCCTGCCTTCGAAATCGTGAA
GGTGAAGAGGTCAAGGATGCTTTGCTAAATCCAAACTGGCATTGCCCACCTTGTCGAGGAATCTGCAACTGCAGCTTCTG
CCGCCAACGAGTTGGACGGTGTGCAACTGGGGTCCTTGTGTATTTAGCCAAGTATCATGGCTTTGGGAGTGTTCATGATT
ACTTGAAAAGCCTGAAACAGGAATTTGAAATGCAAGCG

Alignment

ORF - retro_itri_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 89.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ANTRSQANREGCKTRSHQYKLSGPLRVAMKFPARNTRSAANKKVAPTKPSENFTIDSNSDSEDESGMN-F
          AN......R....TRS.QY.LSGPLRVAMKFPA.NTRSAANKKVAP.KPSENFT.DS.SDSEDESGMN.F
Retrocopy ANQEGCKTRSQDRTRS-QYRLSGPLRVAMKFPAGNTRSAANKKVAPPKPSENFTTDSDSDSEDESGMN>F

Parental  L-EKRALNIKQNKAMLAKLMSELESFPGSFPGRRSLPGPRSVN-SKTPRRRTFPGVASRRNPDRRAR---
          L.EK....IKQNKAM.AKLMSELESFPGSFPGR.SLPGPRSVN.SKTP.RRTFPGVASRRNPD.......
Retrocopy L>EKGFTYIKQNKAMFAKLMSELESFPGSFPGRCSLPGPRSVNESKTP*RRTFPGVASRRNPDPESSDWS

Parental  PLTRSRSRILGSLSALPTEEEEEEEEDDKFMLVRKRKTVDGYMNDDDTPRSRRPGSMTLPHIIRPVEEIT
          PL.RSRSRILGSLSALPTEEEEEEEEDDKFMLVRKRKTVD.YMNDDD.PRSRRPGSMTLP.IIRP.EEIT
Retrocopy PLSRSRSRILGSLSALPTEEEEEEEEDDKFMLVRKRKTVDRYMNDDDRPRSRRPGSMTLPQIIRPGEEIT

Parental  EDELENICSNSREKIYNRSLGSTCHQCRQKTIDTKTNCRNPDCWGIRGQFCGPCLRNRYGEEVKDALLNP
          EDEL.NICSNSREKI.NRSLG.TCHQC.QKTIDTKTNCRN..CWG..GQFCGPCLRNR.GEEVKDALLNP
Retrocopy EDELGNICSNSREKI*NRSLGPTCHQCGQKTIDTKTNCRNLGCWGTQGQFCGPCLRNREGEEVKDALLNP

Parental  NWHCPPCRGICNCSFCRQRDGRCATGVLVYLAKYHGFGNVHDYLKSLKQEFEMQA
          NWHCPPCRGICNCSFCRQR.GRCATGVLVYLAKYHGFG.VHDYLKSLKQEFEMQA
Retrocopy NWHCPPCRGICNCSFCRQRVGRCATGVLVYLAKYHGFGSVHDYLKSLKQEFEMQA

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_369 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_369 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369 ,