RetrogeneDB ID: retro_itri_1845

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394053.1:105071..105679(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM38B
• Ensembl ID: ENSSTOG00000003014
• Aliases: None
• Description: transmembrane protein 38B [Source:HGNC Symbol;Acc:25535]

Sequence

>retro_itri_1845
ATGGACTCTCCATGGGAGGAGCTGGCACTGGCCTTCTCCTGCACATCCATGTTCCCCTTTTTTGACATCACCCACATCTG
GTGTCTTTGATGGCACTGAAACATCAGCCAGTAGGAGTGGAAGGGGCATGGAAGAATCCTGTTTCAAGCTGGTCTACTGC
TGTGCTCCACTGCTTTGGTGGAGGAATTTTAACATGTGTACTGCTTGAAGAGCCTCTGCTGAGGTTTCTTCCAAACCACA
TTAATATTTTACTGGCATCTTCAATCTGGTATATTATATATATTTTTTTGCCCATGGGACCTAAATTCCCAGGACTATTC
ATTCTTATCTGCTCAACTTCTGGCTTTGGGGTTGAAGGAAGTGACCAGAACTTGGAAAATAGAAGGTGGAGTCACACATG
CTAATAGTTATTACAAAAATGGCTGGCCAGTCATGATAGCTATTGGATGGGCCCAAGGTGCAGAGGGTATCCTTATCATG
AATTTTTAATGGCTAGTGAAAGGTGATTAGAAACCAGAGATGATGAATGGCTGTAAATGTCCTATCCTTCCAAGGTAACC
TTGCTGGGGTCCCTTCACATTTCAGCACACCAAGCATCTGACCACATC

Alignment

ORF - retro_itri_1845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 69.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDSSWEDLTLAFSRTSMFPFFDIAH-YLVSVMALKHRPGAVEGAWKNPFSSWFTAMLHCFGGGILSCILL
          MDS.WE.L.LAFS.TSMFPFFDI.H..LVS.MALKH.P..VEGAWKNP.SSW.TA.LHCFGGGIL.C.LL
Retrocopy MDSPWEELALAFSCTSMFPFFDITH<HLVSLMALKHQPVGVEGAWKNPVSSWSTAVLHCFGGGILTCVLL

Parental  AEPPLRFFANHTNVLLASSIWYIIF-FCP-WDLISQGYSFLPVQLLAAGMKEVTRTWKIIGGITHANSYY
          .EP.LRF..NH.N.LLASSIWYII..F.P.WDL.SQ.YSFL..QLLA.G.KEVTRTWKI.GG.THANSYY
Retrocopy EEPLLRFLPNHINILLASSIWYIIYIFLP>WDLNSQDYSFLSAQLLALGLKEVTRTWKIEGGVTHANSYY

Parental  KNGWLVMIAIGWAQGAGGIIITNFEQLLKGDWKPE-GNEWLKMSYPSKVTLLGSL-IFTFQHTKHL
          KNGW.VMIAIGWAQGA.GI.I.NF..L.KGD.KPE...EWL.MSYPSKVTLLGSL.I...Q...H.
Retrocopy KNGWPVMIAIGWAQGAEGILIMNF*WLVKGD*KPE<DDEWL*MSYPSKVTLLGSLHISAHQASDHI

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_1845 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1845 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 2 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002467	1 retrocopy	retro_chof_1110,
Ictidomys tridecemlineatus	ENSSTOG00000003014	7 retrocopies	retro_itri_1553, retro_itri_1708, retro_itri_1789, retro_itri_1823, retro_itri_1824, retro_itri_1826, retro_itri_1845 ,