RetrogeneDB ID: retro_itri_988

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393356.1:3594049..3594359(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP1LC3A
• Ensembl ID: ENSSTOG00000006158
• Aliases: None
• Description: microtubule-associated protein 1 light chain 3 alpha [Source:HGNC Symbol;Acc:6838]

Sequence

>retro_itri_988
AGATGTGAGATTCGTCCAAGAGCAGATTCCATTCAGATCCCAATCCCTATGATAACAGAACAACACAAGGTGAGAGGCAG
CTGCCCATCCTGGATAAAACCAAGTTCCTGGTATTTGACCATATCAACATGGGCAAGCTCATCAGGATAACTAGAAGGTG
CTTACAGCTCAATGTTCATCAAGGCTTCTTCCTTTTGGTAAACCAAGAAACATGGTGAGTGTGTCCTTGCCCATCTCCAA
GGGGCACGAGAGTGAGAAGGATGAAGCTGGATTCTTCCTGTGTGTGGTGTATAACTCCCAGAAGATGTTC

Alignment

ORF - retro_itri_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RCKEVQQIRDQHPSKIPVIIERYK-GEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVN
          RC.E.....D.....IP.I.E..K.GE.QLP.LDKTKFLV.DH.NM..L..I.RR.LQLN..Q.FFLLVN
Retrocopy RC-EIRPRADSIQIPIPMITEQHK<GERQLPILDKTKFLVFDHINMGKLIRITRRCLQLNVHQGFFLLVN

Parental  Q-HSMVSVSTPIADIYEQEKDEDG-FLYMVYASQETF
          Q...MVSVS.PI....E.EKDE.G.FL..VY.SQ..F
Retrocopy Q<RNMVSVSLPISKGHESEKDEAGFFLCVVYNSQKMF

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_988 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_988 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012407	1 retrocopy	retro_etel_1766,
Felis catus	ENSFCAG00000022040	1 retrocopy	retro_fcat_1634,
Monodelphis domestica	ENSMODG00000002694	1 retrocopy	retro_mdom_1256,
Mustela putorius furo	ENSMPUG00000017814	1 retrocopy	retro_mputfur_1049,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Ictidomys tridecemlineatus	ENSSTOG00000006158	2 retrocopies	retro_itri_287, retro_itri_988 ,
Ictidomys tridecemlineatus	ENSSTOG00000014826	2 retrocopies	retro_itri_1505, retro_itri_662,