RetrogeneDB ID: retro_itri_1795

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393799.1:351720..352579(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010929
• Aliases: None
• Description: None

Sequence

>retro_itri_1795
CTGGCCTGGCCGAGTGTTTTCCAAAGAGGGACTGTGCTCTTGCGGTTTCAGCCATCACCATGTGGTTGTATTCCTGCTCA
CCCTCTTCATTTATTCATTGCTCCATGCTTCAAGAAAAACATTTAGCAATGTCAAAGTTAGTATCTCCAAGCAGTGGACC
CCAATTGCTTTTAACACAACACTTGAGCTGCCTGTAGAGATCTGGAGCAGCAACCATTTATTTCCCAATACAGAGGAGGC
TACTCTTTTCTGTGGAATACTGGATACTATTTTTCTGTTCTCCTACGCTGTGGGTCTTTTCATCAGTGGCATGGTTGGGG
ATAGGCTGAATTTACAATGGGTTCTCTCTATTGGCATGTGCTCTTCTGCATTATTGGTGTTTGTCTTTGGCACTCTCACA
GAATGGCTGCACTTCTACAACAGATGGTTCTATTGTTGCCTGTGGATTGTGAATGGCCTGTTGTAGTCCACTGGCTGGCC
CTGTGTGGTTGCTGTGATGGGCAACTGGTTTGGGAAAAATGGGCAAGGAGTTGTCTTTGGTCTCTGGAGTGCCTGTGCTT
CTGTGGGCAATATTTTGGGAGCATGTCTAGCTTCATCTGTTCTACAGTATGGTTATGAGTATGCCTTTCTGGTGACAGCG
ACTGTGCAGTTTGCTGGTGGGATTGTCATCTTCTTTGGACTCCTGGTGTCACCAGAAGAAATTGGTCTCCCAGGTATTGA
AGTAGAAGAAAATTTTGAAGAAGATTCCCACAGACTGTTAATTAATGGTACTGAAAACGAAGATGAATATGAGCCTAATT
ACTCTATCCAAGAGTCCAGAACTGTTGCCCAAGTGAAGGCAATAAGCTTCTACCAGGCT

Alignment

ORF - retro_itri_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.73 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAWPSVFQRGTVLSRF-SHHHVVVFLLTFFSYSLLHASRKTFSNVKVSISKQWTPNAFNTTLELPVEIWS
          .AWPSVFQRGTVL.RF.SHHHVVVFLLT.F.YSLLHASRKTFSNVKVSISKQWTP.AFNTTLELPVEIWS
Retrocopy LAWPSVFQRGTVLLRF>SHHHVVVFLLTLFIYSLLHASRKTFSNVKVSISKQWTPIAFNTTLELPVEIWS

Parental  SNHLFPNTEEATLFLGTLDTIFLFSYAVGLFISGIVGDRLNLRWVLSFGMCSSALVVFVFGTLTEWLHFY
          SNHLFPNTEEATLF.G.LDTIFLFSYAVGLFISG.VGDRLNL.WVLS.GMCSSAL.VFVFGTLTEWLHFY
Retrocopy SNHLFPNTEEATLFCGILDTIFLFSYAVGLFISGMVGDRLNLQWVLSIGMCSSALLVFVFGTLTEWLHFY

Parental  NRWLYCCLWIVNGLLQSTGWPCVVAVMGNWFGKNGRGVVFGLWSACASVGNILGACLASSVLQYGYEYAF
          NRW.YCCLWIVNGLL.STGWPCVVAVMGNWFGKNG.GVVFGLWSACASVGNILGACLASSVLQYGYEYAF
Retrocopy NRWFYCCLWIVNGLL*STGWPCVVAVMGNWFGKNGQGVVFGLWSACASVGNILGACLASSVLQYGYEYAF

Parental  LVTASVQFAGGIVIFFGLLVSPEEIGLPGIEAEENFEEDSHRPLINGTENEDEYEPNYSIQESRTVAQVK
          LVTA.VQFAGGIVIFFGLLVSPEEIGLPGIE.EENFEEDSHR.LINGTENEDEYEPNYSIQESRTVAQVK
Retrocopy LVTATVQFAGGIVIFFGLLVSPEEIGLPGIEVEENFEEDSHRLLINGTENEDEYEPNYSIQESRTVAQVK

Parental  AISFYQA
          AISFYQA
Retrocopy AISFYQA

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_1795 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1795 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
Bos taurus	ENSBTAG00000012239	1 retrocopy	retro_btau_1471,
Canis familiaris	ENSCAFG00000003973	1 retrocopy	retro_cfam_2207,
Mus musculus	ENSMUSG00000029924	1 retrocopy	retro_mmus_3670,
Ictidomys tridecemlineatus	ENSSTOG00000010929	1 retrocopy	retro_itri_1795 ,
Tursiops truncatus	ENSTTRG00000009525	1 retrocopy	retro_ttru_921,