RetrogeneDB ID: retro_itri_1875

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394312.1:58077..58946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF207
• Ensembl ID: ENSSTOG00000000712
• Aliases: None
• Description: zinc finger protein 207 [Source:HGNC Symbol;Acc:12998]

Sequence

>retro_itri_1875
GGATTGCATCATCAGAGAAAATACACCCAGTCATTTTGTGGTGAAACCATAATGATGCCAATGGGTGGAATGATGACACC
TGAACCAGGAATACCACCTCTTATGCCTGGTATGCCACCAGGTATGCCCCCCCCATTCCCTGTCCTGGAATTCCTTCAAT
GACTCAAGTACAGGCTGTGTAAGCATCAGGTATTCTTAATAGGCCACCTGCACCAACAGCAACAGTACCTGCTCCACAGC
CTCCAGTAACTAAGCCTCTTTTTCCCAGTGCTGGACAAATGGGGACACCTGTAACAAGCTCAAGTATAGCTTCATCCAAT
TCATAAAGTCTTTCTACATCTTCTAAAGCTCTGTTTCCTAGCATAGCACAAGCTCAGGCAGCTGTGCAAGGACCTGTTGG
TACAGATATCAAGCCCTTAAATAGCACCCCTGCAACAATTACAGAACCCCCAAAGCCTACATTCCCTGCTTATACACAGT
CTACAGCTTCAACCACTAGGACAACAAATAGTACTGCAGCAAAACCAGCAGCTTCAATAACAAGTAAGCTTGCTACACTT
ACAACCACCAGTGCAACCAGTAAGTTGATCCATCCAGATGAGGATTTATCACTGGAAGAGAGAAGGGCACAGTTACATAA
TTATCAGCATAATCTTCCTCGACTAGGACAGGCCCCAATCAGTAACCCACCAGTTGGACCAATTGGAGGTATAATGCCAC
CACAGCCAGGCATCCCACAGCAGCAAGGAATGAGACCCACAATGCCACCTCATGGTCAGTATGGTGGTCATCATCAAGGC
ATGCCAGGTTACCTTCCTGGTGCTATGCCACCATATGGGCAGCGACCACCAATGGTACCCAATAACCAA

Alignment

ORF - retro_itri_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89. %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLHHQRKYTQSFCGENIMMPMGGMMPPGPGIPPLMPGMPPGMPPP-VPRPGIPPMTQAQAVSAPGILNRP
          GLHHQRKYTQSFCGE.IMMPMGGMM.P.PGIPPLMPGMPPGM.....P.PGIP.MTQ.QAV.A.GILNRP
Retrocopy GLHHQRKYTQSFCGETIMMPMGGMMTPEPGIPPLMPGMPPGMXXX<IPCPGIPSMTQVQAV*ASGILNRP

Parental  PAPTATVPAPQPPVTKPLFPSAGQMGTPVTSSSTASSNSESLSASSKALFPSTAQAQAAVQGPVGTDFKP
          PAPTATVPAPQPPVTKPLFPSAGQMGTPVTSSS.ASSNS.SLS.SSKALFPS.AQAQAAVQGPVGTD.KP
Retrocopy PAPTATVPAPQPPVTKPLFPSAGQMGTPVTSSSIASSNS*SLSTSSKALFPSIAQAQAAVQGPVGTDIKP

Parental  LNSTPATTTEPPKPTFPAYTQSTASTTSTTNSTAAKPAASITSKPATLTTTSATSKLIHPDEDISLEERR
          LNSTPAT.TEPPKPTFPAYTQSTASTT.TTNSTAAKPAASITSK.ATLTTTSATSKLIHPDED.SLEERR
Retrocopy LNSTPATITEPPKPTFPAYTQSTASTTRTTNSTAAKPAASITSKLATLTTTSATSKLIHPDEDLSLEERR

Parental  AQLPKYQRNLPRPGQAPIGNPPVGPIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGMPGYLPGAMPPY
          AQL..YQ.NLPR.GQAPI.NPPVGPIGG.MPPQPGIPQQQGMRP.MPPHGQYGGHHQGMPGYLPGAMPPY
Retrocopy AQLHNYQHNLPRLGQAPISNPPVGPIGGIMPPQPGIPQQQGMRPTMPPHGQYGGHHQGMPGYLPGAMPPY

Parental  GQGPPMVPPYQ
          GQ.PPMVP..Q
Retrocopy GQRPPMVPNNQ

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_1875 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1875 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001728	1 retrocopy	retro_cpor_1464,
Echinops telfairi	ENSETEG00000003828	1 retrocopy	retro_etel_883,
Homo sapiens	ENSG00000010244	1 retrocopy	retro_hsap_2373,
Myotis lucifugus	ENSMLUG00000016085	1 retrocopy	retro_mluc_322,
Nomascus leucogenys	ENSNLEG00000005954	1 retrocopy	retro_nleu_362,
Otolemur garnettii	ENSOGAG00000001200	2 retrocopies	retro_ogar_33, retro_ogar_751,
Pongo abelii	ENSPPYG00000008161	1 retrocopy	retro_pabe_2144,
Pan troglodytes	ENSPTRG00000008989	1 retrocopy	retro_ptro_1735,
Ictidomys tridecemlineatus	ENSSTOG00000000712	2 retrocopies	retro_itri_1800, retro_itri_1875 ,