RetrogeneDB ID: retro_itri_1759

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393727.1:473505..473922(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025976
• Aliases: None
• Description: None

Sequence

>retro_itri_1759
AAGAGGATGGCCACGGTGTACGTTTGCGGCATGGAGTACCTGCTGTTCACCAGCAGACCCTTCCTGTGGAACCTGACAGT
GTACACGCTCTGGAGATGGCCTACAGAGCGGCTGCTGGCTTGCCACAAGGTGCTGCAGATATGTGCAGGTTGCAGATGTG
TACCAGATGACAGAGGAAAGGCACTGCCAGGTGCACCTTCTGGATGACAGAAGGCTGGAGCTGCTGGTTCAGCCCAAACT
TCTGTCAAGAGAGCTCCTGGATTTGATGGTTTCACACTTCAACCTGAAATAAAAGAGTACTTTTTGTTCATAGATGACAC
TGGTCAGCAGAACTGGCTGCAGTTGGACCACCGAGTACTGGATCATGACTTGCCCAAAAAGCCGGGCCCAGCCGCCTTGC
ACCTTGCCATCAGGTTC

Alignment

ORF - retro_itri_1759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 52.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRMASVFTCGVEDLLFAGSRFVWNLTVTTLRRWSSERLRACHQVLRTWCG-LRDVYQMTEGRHCQVHLLD
          .RMA.V..CG.E.LLF....F.WNLTV.TL.RW..ERL.ACH.VL...C....DVYQMTE.RHCQVHLLD
Retrocopy KRMATVYVCGMEYLLFTSRPFLWNLTVYTLWRWPTERLLACHKVLQI-CA>VADVYQMTEERHCQVHLLD

Parental  DRRLELLVQPKLLSRELLDLVASHFNLK-EKEYFGITFTDDTGQQNWLQLDHRVLDHDLPKKPGPAALQF
          DRRLELLVQPKLLSRELLDL..SHFNLK..KEYF...F.DDTGQQNWLQLDHRVLDHDLPKKPGPAAL..
Retrocopy DRRLELLVQPKLLSRELLDLMVSHFNLK<IKEYF--LFIDDTGQQNWLQLDHRVLDHDLPKKPGPAALHL

Parental  AVRF
          A.RF
Retrocopy AIRF

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_1759 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1759 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000025976	6 retrocopies	retro_itri_1757, retro_itri_1759 , retro_itri_1778, retro_itri_1781, retro_itri_1782, retro_itri_186,