RetrogeneDB ID: retro_itri_1381

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393468.1:3031180..3031563(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR2
• Ensembl ID: ENSSTOG00000028971
• Aliases: None
• Description: signal sequence receptor, beta (translocon-associated protein beta) [Source:HGNC Symbol;Acc:11324]

Sequence

>retro_itri_1381
GCATTAGATGTGGAATTATCTGATGATTCCTTCCCTCCAGAAGACATTGGCATTGTTTTCTGGTTTACTCATTGTCGAAT
GATACCAGATTGCCCCTGCTAACAATCTCTCCCACAATGTAGTCCTGCATCCTCTCAAGTCTGGTTACTTCAACTTCAAC
TCTGAAACAATTACTTACCTGACCCAGGAGGATGGACATGTTATGGCTGGCTCCATCAATGCACTTGGACAGGAAGAAAT
CCTGGCTCAGGGGCAGTTTGATAGGGATCCTCCCCACTTTTCTTGACTGGGCAGCCTTTGGTTTTATGACCCTTCCATCC
ATTGGCATCCCCCTACTCATGTGGTATTCCAGCAAGAGAAAATAGGACACTTCCATAACCAAG

Alignment

ORF - retro_itri_1381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 70.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALDVELSDDSFPPEDFGIV-SGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATITYLAQEDGPVVV
          ALDVELSDDSFPPED.GIV.SG.L.V....IAPA.N.SH.VVL.PLK.GYFNF.S.TITYL.QEDG.V..
Retrocopy ALDVELSDDSFPPEDIGIV>SGLLIVE*YQIAPANNLSHNVVLHPLKSGYFNFNSETITYLTQEDGHVMA

Parental  GSTSAPGQGGILAQREFDRRFSPH-FLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKTK
          GS..A.GQ..ILAQ..FDR...PH.FLDWAAFG.MTLPSIGIPLL.WYSSKRK.DT..TK
Retrocopy GSINALGQEEILAQGQFDRD-PPH>FLDWAAFGFMTLPSIGIPLLMWYSSKRK*DTSITK

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_1381 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1381 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001212	2 retrocopies	retro_btau_1165, retro_btau_675,
Cavia porcellus	ENSCPOG00000023729	1 retrocopy	retro_cpor_478,
Nomascus leucogenys	ENSNLEG00000012304	1 retrocopy	retro_nleu_3102,
Ictidomys tridecemlineatus	ENSSTOG00000028971	1 retrocopy	retro_itri_1381 ,