RetrogeneDB ID: retro_itri_1578

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393553.1:1031903..1032860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSSTOG00000014262
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_itri_1578
GGAATTCTACATATGGAGGCCCGGTTGGCAGAGAGGAAATTCATGAACCCTTTCAACATGCCTAATCTTTATCAGAAGTT
GGAGAGTGATCCCAGGACAAGGGCACTGCTTAGTGATCCTACCTACCGGGAACTGATAGAGCAACTAGGAAACAAACCGT
CAGACTTGGCCATGACACTACAAGATCCCCGGATCATAACCACTCTCAGTGTCCTCATTGGGGTTGATCTGGGCAGCATG
GATGAGGAAGAAGAGGCTGCAACACCCCCGCCTCCACCTCCCTGCAAAAAGGAAACCAAGCCAGAGCCAATGGAAGAAGA
TCTCCCAGAGAATAAGAAGCAGGCACTGAAAGAAAAAGAACTGGGGAATGATGCCTACAAGAAGAAAGACTTTGACTCAG
CCCTGAAGCACTACGACAGGGCCAAGGAGCTGGACCCCACCAACATGACTTACATTACCAATCAAGCAGTGGTATACTTT
GAAAAGGGCGACTACAATAAATGCCGGGAGCTTTGTGAGAAGGCCATCGAGGTGGGGAGAGAGAACCGAGAAGACTATCG
ACAGATTGCCAAAGCTTATGCTCGAATTGGTAACTCCTACTTCAAAGAGGAAGCGTACAAGGACGCTATCCATTTCTACA
ACAAATCACTGGCAGAGCACCAAATCCCAGATGTGATCAAGAAATGCCAGCAGGCAGAGAAAATTCTGAAGGAGCAAGAG
CAACTGGTCTACAACAACCTCGACCTGGCATTGGAGGAGAAGAACAAGGGCAATGAGTGTTTTCAGAAAGGGGACTATCC
CCAGGCCATGAAGCACTATACAGAAGCCATTAAACGGAATACACGAGATGCCAAACTGTACAGTAATCGAGCTGCCTGCT
ACACCAAACTCCTGGAGTTTCAGCTGGCACTCAAGGACTGTGAGGAATGTATCCAGCTGGAGCCAACTTTCATCAAG

Alignment

ORF - retro_itri_1578 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.3 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLQNMEARLAERKFMNPFNMPNLYQKLESDPRTRALLSDPTYRELIEQLRNKPSDLAMKLQDPRIITTLS
          G...MEARLAERKFMNPFNMPNLYQKLESDPRTRALLSDPTYRELIEQL.NKPSDLAM.LQDPRIITTLS
Retrocopy GILHMEARLAERKFMNPFNMPNLYQKLESDPRTRALLSDPTYRELIEQLGNKPSDLAMTLQDPRIITTLS

Parental  VLIGVDLGSMDEEEEAATPPPPPPPKKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDSALKHYDR
          VLIGVDLGSMDEEEEAATPPPPPP.KKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDSALKHYDR
Retrocopy VLIGVDLGSMDEEEEAATPPPPPPCKKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDSALKHYDR

Parental  AKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEAYKDAI
          AKELDPTNMTYITNQA.VYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEAYKDAI
Retrocopy AKELDPTNMTYITNQAVVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEAYKDAI

Parental  HFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRN
          HFYNKSLAEH..PDV.KKCQQAEKILKEQE.L.Y.N.DLALEEKNKGNECFQKGDYPQAMKHYTEAIKRN
Retrocopy HFYNKSLAEHQIPDVIKKCQQAEKILKEQEQLVYNNLDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRN

Parental  PRDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIK
          .RDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIK
Retrocopy TRDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIK

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_1578 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1578 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578 ,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,