RetrogeneDB ID: retro_itri_1796

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393802.1:4723..5506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA7
• Ensembl ID: ENSSTOG00000012433
• Aliases: None
• Description: annexin A7 [Source:HGNC Symbol;Acc:545]

Sequence

>retro_itri_1796
AGAGCAGCTTTTAAGACCATGTATGGCAAGGATTTAATCAAAGATCTCAAGTCAGAGTTGAGTAGAAATGTGTAAGAACT
GATTATTTCCCTGTTCCTGCCTCCTACATATTATGATGCCTGAAGTTTATGGAATGCAATGCAGGGAGCAGAAACTCAGG
AACATGTATTGATACAGATTTTGTGCACAAGAACAAATCAAGAAATCCAAGAAACTGTCATATGTTATCAATCAGAATTT
GGAAGAGACTTTGAAAAGGACATTAGGTCAGATACATCTGAACGGTTGCTTGTATCCACGGTCAGGGAAATTGTGATGAG
AATCAGAGTGCAAACCTCCAAATGGCTCAAGAAGATGTCAGTGTCTCTATAAAGCTGGTCAGGGGAGACTAGGGACAGAT
GGATCTTGCTTTAACATGATCCTTGTCACAAGAAGCTTTCCTCAGCTGAAAGCTACTATGGAATCTTATTCCAGGATTTC
TTATCAAGATTTGTTAAGCAGTGTGGGCCTGGAGTTTTCTGGATAGGTTGAAAGTAGTTTGAAGACCATCTTGAAATGTA
CCCGAACTGTCCTGCCTTCTTTGCTGAGTGGCTGTATTATTCCATGAAAGGTACAGGCTCATACAACTCCACTCTGGTCA
AGATTGTGACCTCTCAATCTGAGATTGAACTTGTACCAATAAAACAGATGTTCAATCAGATGTATCAGAAGCCCTTGGGC
ACAATGATTGGGAGTGACACAATTAGAGATTACTGAAAGCTGCTTCTGGCCATTGTGGGTCAG

Alignment

ORF - retro_itri_1796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.49 %
• Parental protein coverage: 54.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KAAFKTMYGKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRNAMQGAGTQERVLIEILCTRTNQEIR
          .AAFKTMYGKDLIKDLKSELS.N..ELI..LF.PPTYYDA.SL.NAMQGA.TQE.VLI.ILCTRTNQEI.
Retrocopy RAAFKTMYGKDLIKDLKSELSRNV*ELIISLFLPPTYYDA*SLWNAMQGAETQEHVLIQILCTRTNQEIQ

Parental  DIVRCYQTEFGRDLEKDIRSDTSGHFERLLVSMC-QGNRDENQSVNHQMAQED-AQRLYQAGEGRLGTDE
          ..V.CYQ.EFGRD.EKDIRSDTS...ERLLVS...QGN.DENQS.N.QMAQED..Q.LY.AG.GRLGTD.
Retrocopy ETVICYQSEFGRDFEKDIRSDTS---ERLLVSTV<QGNCDENQSANLQMAQED<CQCLYKAGQGRLGTDG

Parental  SCFNMILATRSFPQLKATMEAYSRMSNRDLLSSVGREFSGYVESGLKTILQCAL-NRPAFFAERLYYSMK
          SCFNMIL.TRSFPQLKATME.YSR.S..DLLSSVG.EFSG.VES.LKTIL.C...N.PAFFAE.LYYSMK
Retrocopy SCFNMILVTRSFPQLKATMESYSRISYQDLLSSVGLEFSG*VESSLKTILKCTR<NCPAFFAEWLYYSMK

Parental  GAGTDDSTLVRIVVSRSEIDLVQIKAMFTQMYQKTLGTMIASDTSGDYRKLLLAIVGQ
          G.G...STLV.IV.S.SEI.LV.IK.MF.QMYQK.LGTMI.SDT..DY.KLLLAIVGQ
Retrocopy GTGSYNSTLVKIVTSQSEIELVPIKQMFNQMYQKPLGTMIGSDTIRDY*KLLLAIVGQ

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_1796 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1796 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014749	1 retrocopy	retro_cfam_1107,
Callithrix jacchus	ENSCJAG00000001720	3 retrocopies	retro_cjac_1288, retro_cjac_2174, retro_cjac_860,
Microcebus murinus	ENSMICG00000013143	2 retrocopies	retro_mmur_404, retro_mmur_884,
Pteropus vampyrus	ENSPVAG00000013001	1 retrocopy	retro_pvam_1365,
Rattus norvegicus	ENSRNOG00000007136	1 retrocopy	retro_rnor_2446,
Ictidomys tridecemlineatus	ENSSTOG00000012433	1 retrocopy	retro_itri_1796 ,