RetrogeneDB ID: retro_itri_1421

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393482.1:1851552..1851862(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMGT1
• Ensembl ID: ENSSTOG00000004796
• Aliases: None
• Description: membrane magnesium transporter 1 [Source:HGNC Symbol;Acc:28100]

Sequence

>retro_itri_1421
TCTTATATGCAATTAACAGATAAAGAAGATGAATCACTGCCAATAGATGTAGTTCTTCAGATACTTCTGGCCTTTGCAGT
TACCTGTTATGGTATAGTTCATATTGCAGGAGAGTTTAAAGACATGGATGCCACTTCAGAACTAAAAAAATAAGACATTT
GATACCTTAAGGAATCACACATCATTTTATGTATTTAATCATCGTGGTCGAGTACTGTTCCGGCCTTCAGATACAACAAA
TTCCTCAAACCAGGAGGCATTGTCCTCTAACACATCATTGAAGTTATGAAAACTCGAATCACTGCTCCGC

Alignment

ORF - retro_itri_1421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 78.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SYMRLTEKEDESLPIDXXXXTLLAFAVTCYGIVHIAGEFKDMDATSELK-NKTFDTLRNHPSFYVFNHRG
          SYM.LT.KEDESLPID.....LLAFAVTCYGIVHIAGEFKDMDATSELK.NKTFDTLRNH.SFYVFNHRG
Retrocopy SYMQLTDKEDESLPIDVVLQILLAFAVTCYGIVHIAGEFKDMDATSELK>NKTFDTLRNHTSFYVFNHRG

Parental  RVLFRPSETTNSSNQEALSSNTSLKLRKLESLRR
          RVLFRPS.TTNSSNQEALSSNTSLKL.KLESL.R
Retrocopy RVLFRPSDTTNSSNQEALSSNTSLKL*KLESLLR

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_1421 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1421 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421 ,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,