RetrogeneDB ID: retro_itri_1303

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393433.1:2382072..2382489(+)
• Located in intron of: ENSSTOG00000003897

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOSPD1
• Ensembl ID: ENSSTOG00000008152
• Aliases: None
• Description: motile sperm domain containing 1 [Source:HGNC Symbol;Acc:25235]

Sequence

>retro_itri_1303
ATGCATCAACAAAAAAGACAACCAGAGCTAGTGGAAGGAAATCTTCCCGTGTTTGTGTTTCCCACAGAGCTAATATTTTA
TGCAGATGATCAGTCAACACATAAACAAGTGTTGACGCTGTACAATCCCTATGAGTTCGCCTTGAAGTTCAAAGTTTTGT
GTACTACTCCAAATAAGTATGTTGTCATTGATGCTGTGGGTGCAGTAAAGCCTCGGTGTTGTGTGGATATTGTGATTCGT
CATAGAGATGTTTGATCCTGTCACTATGGTGTAATAGATAAATTCCGTCTCCAAGTTTCTGAGCAAAGCCAGAGGAAGGC
TTTAGGAAGGAAAGAGGTTGTTGCTACTCTTCTCCCATCTGCAAAAGAACAACAAAAGGAAGATGAGCAAAAAAGACTAA
AGGAACATTTAACTGAA

Alignment

ORF - retro_itri_1303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.68 %
• Parental protein coverage: 64.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
          MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVV.DA.GAVK
Retrocopy MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVIDAVGAVK

Parental  PQCCVDIVIRHRDVRSCHYGVIDKFRLQVSEQSQRKALGRKEVVATLLPSAKEQQKEDEEKRIKEHLTE
          P.CCVDIVIRHRDV.SCHYGVIDKFRLQVSEQSQRKALGRKEVVATLLPSAKEQQKEDE.KR.KEHLTE
Retrocopy PRCCVDIVIRHRDV*SCHYGVIDKFRLQVSEQSQRKALGRKEVVATLLPSAKEQQKEDEQKRLKEHLTE

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_1303 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1303 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303 ,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,