RetrogeneDB ID: retro_itri_1194

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393397.1:5939484..5939829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SS18
• Ensembl ID: ENSSTOG00000015699
• Aliases: None
• Description: synovial sarcoma translocation, chromosome 18 [Source:HGNC Symbol;Acc:11340]

Sequence

>retro_itri_1194
GCCAATGGATCCATGGGAGGTTACAACCATTCTGTGCCATCATCACAGAGCATGCCAGTACAGAATCAGATGACAATGAG
TCAAGGGCAGCCAATGGGAAACTATGGCCCACGATCAAATGTGAATATGCAACAAAACCAAGGCCCAATGATGCATCAGC
AGCCCCCTTCTCAGCAGTACAGTATGCCACAAGGATATGGGCATCATTACCAAGGACAGCAGCCACCCATGGGAATGAGG
GGTCAAGTTAACCAAGGCAATCATATGATGGGTCAGAAACAGATTCCTCCCTGTAGACCACCTCAACAGGGAAACTCACA
ATATGGCCAACAACAGGATGCTTAC

Alignment

ORF - retro_itri_1194 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 52.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQGGGQHY
          ..GSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPR.N.NMQ.NQGPMMHQQPPSQQY.MPQG.G.HY
Retrocopy ANGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRSNVNMQQNQGPMMHQQPPSQQYSMPQGYGHHY

Parental  QGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYY
          QGQQPPMGM.GQVNQGNHMMGQ.QIPP.RPPQQG...QY..Q.D.Y
Retrocopy QGQQPPMGMRGQVNQGNHMMGQKQIPPCRPPQQG-NSQYGQQQDAY

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_1194 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1194 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000037013	1 retrocopy	retro_mmus_1951,
Ictidomys tridecemlineatus	ENSSTOG00000015699	1 retrocopy	retro_itri_1194 ,
Tupaia belangeri	ENSTBEG00000007668	3 retrocopies	retro_tbel_3879, retro_tbel_4107, retro_tbel_8,