RetrogeneDB ID: retro_itri_472

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:20453745..20454082(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCL1A
• Ensembl ID: ENSSTOG00000002570
• Aliases: None
• Description: T-cell leukemia/lymphoma 1A [Source:HGNC Symbol;Acc:11648]

Sequence

>retro_itri_472
GTCATGGAAGGGTTCTTGTTCAACCCAGAGTATCCTCCAGACCCCTACCACCTGTGGATCTGGAAGAAGGCCTTGTATAT
AGACGAGAACTGGCGCACCTGGATGCCCATCATCATCAAGACAGAGGATAGCTTCAAGGTGAACATGCGCCAGGGAGACC
TCCCCTTGGGGGGCGATCAGAGACCACTGAGCTGACATGAGCCTCCTGACTTTGCTGTGGCAGCTGTACCCTGGAGGAAG
ATACTGAGGCTCAGGCTCCACCCTCTGCCGCATAGTGTACCACATCGAGTACAACAGCATAGAGGACATGCTCCTGGAGT
TGCTGCCGACCCCAGAA

Alignment

ORF - retro_itri_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VMEGFLFEPDYPPDPDRLWRWNMLLYVDETYRTWLPIIIKMEGSLQVLMRQEDYPLESPLSP-SEMT-PS
          VMEGFLF.P.YPPDP..LW.W...LY.DE..RTW.PIIIK.E.S..V.MRQ.D.PL.....P..E.T..S
Retrocopy VMEGFLFNPEYPPDPYHLWIWKKALYIDENWRTWMPIIIKTEDSFKVNMRQGDLPLGGDQRP<TELT<MS

Parental  LLPVLYQLYPERRYRGSDSSLWRIVYHIEYNRVEDMLLEQLPAPE
          LL..L.QLYP..RY.GS.S.L.RIVYHIEYN..EDMLLE.LP.PE
Retrocopy LLTLLWQLYPGGRY*GSGSTLCRIVYHIEYNSIEDMLLELLPTPE

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_472 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_472 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000006953	2 retrocopies	retro_mluc_368, retro_mluc_73,
Ictidomys tridecemlineatus	ENSSTOG00000002570	1 retrocopy	retro_itri_472 ,