RetrogeneDB ID: retro_itri_619

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393306.1:3129623..3130366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGPS1
• Ensembl ID: ENSSTOG00000004263
• Aliases: None
• Description: geranylgeranyl diphosphate synthase 1 [Source:HGNC Symbol;Acc:4249]

Sequence

>retro_itri_619
ATGGAGAAGACTCAAGAAACTGTCCAGAGAATTATTCTGAAGCCCTGCAAGTGCTTACTTCAGTTACCAGGTAAACAAGT
GAAAACCAAACTTTCACAGGCATTCAATCATTGGCTGAAAATTCCAGAAGACAAATTACAGATTAACATTGAAGTGGCAG
AAATGTTGCATATGCCAGTTTACTCATTGAGGACCTCAAAGACAGGTCAAAACTCCAACATGGCTTTCCAGTGGCACACA
GCTTCTATGGAATTCCATCTGTCATCAATTCTGCCAATTATGTATATTTCCTTGGCATAGAGAAAGTCTTAACTCATCAT
CCAGAGGCAGTGAAACTTTTACCCCCTCCCCTCCCCCAGCTATTGGAACTCCATCAGGAACAAGGCCTGGATATGTACTG
GAGGGATAATTACACTTGTCCCACTGAAGGAGAATATCAAGCTATGGTGCTGAAAAGACAGGTGGACTGCTGGGATTATT
AGTAGGTCTCATGCAATTTTTCTCTGACTACAAATATTTAAAGCCATTATGTAATACACTTGGGTTCTTTTTAAAATTAG
ACATGATTATGCTGATCAGCACTCCAAAGAATACAGTGAAAACAAAAAAGGTTTTGTGAAGATCTCACAGAGGGAAAATT
CTCATTCCTTATTATTCATGCTATTTGGTCAAGGCCTGAAAGCACCCAGGTGCAGAACATCTTATGGCTGCAGAAAACCC
AGATATTAAAAAAAATATTATGT

Alignment

ORF - retro_itri_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.16 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MEKTQETAQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLH-NASLLIDDIEDN
          MEKTQET.QRI.L.P.K.LLQLPGKQV.TKLSQAFNHWLK.PEDKLQI.IEV.EMLH..ASLLI.D..D.
Retrocopy MEKTQETVQRIILKPCKCLLQLPGKQVKTKLSQAFNHWLKIPEDKLQINIEVAEMLH<YASLLIEDLKDR

Parental  SKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLF---TRQLLELHQGQGLDIYWRDNY
          SKL..GFPVAHS.YGIPSVINSANYVYFLG.EKVLT..HP.AVKL......QLLELHQ.QGLD.YWRDNY
Retrocopy SKLQHGFPVAHSFYGIPSVINSANYVYFLGIEKVLT-HHPEAVKLLPPPLPQLLELHQEQGLDMYWRDNY

Parental  TCPTEEEYKAMVL-QKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLF-FQIRDDYANLHSKEYSENKSF
          TCPTE.EY.AMVL..KTGGL.GL.VGLMQ.FSDYK..LKPL.NTLG.F.F.IR.DYA..HSKEYSENK..
Retrocopy TCPTEGEYQAMVL<EKTGGLLGLLVGLMQFFSDYKY-LKPLCNTLGFF<FKIRHDYADQHSKEYSENKKG

Parental  CEDLTE-GKFSFP-TIHAIWSRPESTQVQNILRQRTENIDIKKYC
          .......GK...P..IHAIWSRPESTQVQNIL......I.....C
Retrocopy FVKISQ>GKILIP>IIHAIWSRPESTQVQNILWLQKTQIXXXXLC

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_619 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_619 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011303	1 retrocopy	retro_cfam_1438,
Echinops telfairi	ENSETEG00000008916	1 retrocopy	retro_etel_1265,
Myotis lucifugus	ENSMLUG00000016813	1 retrocopy	retro_mluc_54,
Mus musculus	ENSMUSG00000021302	1 retrocopy	retro_mmus_1253,
Ictidomys tridecemlineatus	ENSSTOG00000004263	1 retrocopy	retro_itri_619 ,