RetrogeneDB ID: retro_itri_1800

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393822.1:175229..176708(-)
• 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_1800
CTGGGTCACAAGAAGAAGAAGCAGCTGAAGCCGTGGTGCTGGTATTGTAATATAGATTTGATGATGAGAAGATCCTTATA
CAGCACCAAAAGGCAAAGTAGTTTAAATGCCTTATATGTCATAAGAAATTGTATACAGGACCTGGCTTAGCTATTCATTG
CATGCAGGTACATAAAGAGACAATAGATGTTGTACCGAATGCAATACCTGGGAGAATAGACATAGAGTTGGAAATATACG
GTATGAAAGGTATTCTAGAAAAAGATATGGATGAAAGATGACGACTTCTTGAACAGAAAACACAGGAGAGTCAAAAAAGA
AGCAACAGGATGATTCTGATGAGTATGATAATGATGACTCTGCTGCCTCAACTTTATTTCAACCACAGCCTGTTCAACCT
CAGCAATTGTTATATCCCTCCAATGGCTAAGCCAGGACTGTCACCAGTTCCAGGAGCACCAGGAATGCCTCCAGGCATAC
CTCCACTAATGCCAGGTGTTCCTCCTCTGATGCCAGGAATGCCACCAGTTACGCCAGGGATGCCACCTGGATTGCATCAT
CAGAGAAAATTCACCCAGTCATTTTGTGGTGAAAACATAATGATGCCAATGAGTGGAATGATGCCACCTGGACCGAGAAT
ACTACCTCTTATGCCTGGTATGCCACCAGGTATGCCCCCCCCATTCCCTGTCCTGGAATTCCTCCAATACCTAAAGCACA
GGCTGTGTAAGCACCAGGTATTCTTAAAGACCACCTGCACCAACAGCAACAGTACCTGCTCCAGAGCCTCCAGTTACTAA
GCCTCTTTTCCCCAGTGCTGGACAGATAGGTACACCTGTAACAAGCTCAAGTACAGCTTCATCCAATTCAGAAAGTCTGT
CTGCATCTTCTAAAGCTCTGTTTCCTAGCACAGCACAAGCTCAGGCAGCTGTGCAAGGACCTGTTGGTACAGATTTCAAG
CCCTTAAATAGCACCACTGCAACAACTACATAACCCCCAAAGCCTACATTCCCTGCTTATACATAGTCTACAGCTTCAAC
CACTAGTACAACAAATAGTACTGCAGCAAAACCAGCAGCTTCAATAAAAAGTAAGCCTGCTACACTTACAACCACCAGTG
CAACCAGTAAGTCGATCCATCCAGATGAGGATATATCACTGGAAGAGAGAAGGGCACAGTTACCTAAATATCAGAGTTAT
CTTCCTCGACCAGGACAGGCTCCAATTGGTAATCCACCAGTTGAACCAATTGGAGGTATGATGCCACCACAGCCAGGCAT
CCCACAGCAGCAAGGAATGAGACCCCCAATGCCACCTCATGGTCAGTATGGTGGTCATCATCAAGGCATGCCAGGTTACC
ATCCTGGTGCTATGCCACCGTATGGGCAGGGACCACCAATGGTACCCCATTACCAAGGTGGGCCTCCTTGACCTCCAATG
GGAATGAGACCTCCTGTAATGTCGCAAGATGGCCGTTAC

Alignment

ORF - retro_itri_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGRKKKKQLKPWCWYCNRD-FDDEKILIQHQKAKHFKCHICHKKLYTGPGLAIHCMQVHKETIDAVPNAI
          .G.KKKKQLKPWCWYCN.D.FDDEKILIQHQKAK.FKC.ICHKKLYTGPGLAIHCMQVHKETID.VPNAI
Retrocopy LGHKKKKQLKPWCWYCNID<FDDEKILIQHQKAK*FKCLICHKKLYTGPGLAIHCMQVHKETIDVVPNAI

Parental  PGRTDIELEIYGMEGIPEKDMDERRRLLEQKTQESQK-KKQQDDSDEYDDDDSAASTSFQPQPVQPQQ-G
          PGR.DIELEIYGM.GI.EKDMDER.RLLEQKTQESQK.KKQQDDSDEYD.DDSAAST.FQPQPVQPQQ..
Retrocopy PGRIDIELEIYGMKGILEKDMDER*RLLEQKTQESQK<KKQQDDSDEYDNDDSAASTLFQPQPVQPQQ>C

Parental  YIPPMAQPGLPPVPGAPGMPPGIPPLMPGVPPLMPGMPPVMPGMPPGLHHQRKYTQSFCGENIMMPMGGM
          YIPPMA.PGL.PVPGAPGMPPGIPPLMPGVPPLMPGMPPV.PGMPPGLHHQRK.TQSFCGENIMMPM.GM
Retrocopy YIPPMAKPGLSPVPGAPGMPPGIPPLMPGVPPLMPGMPPVTPGMPPGLHHQRKFTQSFCGENIMMPMSGM

Parental  MPPGPGIPPLMPGMPPGMPPP-VPRPGIPPMTQAQAVSAPGILN-RPPAPTATVPAPQPPVTKPLFPSAG
          MPPGP.I.PLMPGMPPGM.....P.PGIPP...AQAV.APGIL..RPPAPTATVPAP.PPVTKPLFPSAG
Retrocopy MPPGPRILPLMPGMPPGMXXX<IPCPGIPPIPKAQAV*APGILK<RPPAPTATVPAPEPPVTKPLFPSAG

Parental  QMGTPVTSSSTASSNSESLSASSKALFPSTAQAQAAVQGPVGTDFKPLNSTPATTTEPPKPTFPAYTQST
          Q.GTPVTSSSTASSNSESLSASSKALFPSTAQAQAAVQGPVGTDFKPLNST.ATTT.PPKPTFPAYT.ST
Retrocopy QIGTPVTSSSTASSNSESLSASSKALFPSTAQAQAAVQGPVGTDFKPLNSTTATTT*PPKPTFPAYT*ST

Parental  ASTTSTTNSTAAKPAASITSKPATLTTTSATSKLIHPDEDISLEERRAQLPKYQRNLPRPGQAPIGNPPV
          ASTTSTTNSTAAKPAASI.SKPATLTTTSATSK.IHPDEDISLEERRAQLPKYQ..LPRPGQAPIGNPPV
Retrocopy ASTTSTTNSTAAKPAASIKSKPATLTTTSATSKSIHPDEDISLEERRAQLPKYQSYLPRPGQAPIGNPPV

Parental  GPIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGMPGYLPGAMPPYGQGPPMVPPYQGGPPRPPMGMRP
          .PIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGMPGY.PGAMPPYGQGPPMVP.YQGGPP.PPMGMRP
Retrocopy EPIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGMPGYHPGAMPPYGQGPPMVPHYQGGPP*PPMGMRP

Parental  PVMSQGGRY
          PVMSQ.GRY
Retrocopy PVMSQDGRY

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_1800 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1800 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,