RetrogeneDB ID: retro_itri_1850

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394116.1:68874..69732(+)
• Located in intron of: ENSSTOG00000023094

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSSTOG00000022608
• Aliases: None
• Description: signal sequence receptor, alpha [Source:HGNC Symbol;Acc:11323]

Sequence

>retro_itri_1850
ATGAGACTCCTCCCCCGCCTGCTTCTGCTGCTCTTGCTGGTATTCCCCGCCACCGTTTTGCTCCGAGGCCGCCCAGCAGG
CTCATTAGCAGTGGCACAGGATCTTACAGAGGATGAAGAAACAGTGGAAGATTCAATAATTGAAGATGAAGACGATGAAG
CTGAGGTAGAAGAAGATGAACCCACAGATTTGGCAGAAGATAAAGAGGAAGAAGATGTATCTGGTGAACCTGAAGCATCA
CCAAGTGCAGATACAACTATCCTGTTTGTGAAAGGAGAAGATTTTCCAGCAAATAACATAGTGAAGTTCTTGGTAGGCTT
TACAAACAAGGGTACAGAAGATTTTATTGTGGAATCCCTAGATGCCTCATTTCGTTATCCTCAGGACTACCAGTTTTATA
TCCAGAATTTCACAGCTCTGCCTCTGAACACTGTAGTGCCACCCCAGAGACAGGCCACTTTTGAGTATTCCTTCATTCCT
GCAGAGCCCATGGGTGGACGACCCTTTGGTCTGGTCATCAATCTGAACTACAAAGACTTAAATGGCAATGTATTCCAAGA
TGCTGTCTTCAATCAAACGGTTACAGTTATTGAAAGAGAAGATGGGTTAGATGGAGAAACAATCTTTATGTATATGTTCC
TTGCTGGTCTTGGACTTCTGGTTGTTATTGGCCTTCATCAACTCCTAGAATCTAGAAAGCGCAAGAGACCCATACAGAAA
GTAGAAATGGGTACATCAAGTCAGAATGATGTTGACATGAGTTGGATTCCTCAAGAAACTTTGAATCAAATCAATAAAGC
TTCACCAAGAAGACTGCCCAGGAAGCAGGCACAGAAGAGATCAGTGGGATCAGATGAG

Alignment

ORF - retro_itri_1850 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLLPRLLLLLLLVFPATVLLRGGPAGSLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLAEDKEE
          MRLLPRLLLLLLLVFPATVLLRG.PAGSLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLAEDKEE
Retrocopy MRLLPRLLLLLLLVFPATVLLRGRPAGSLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLAEDKEE

Parental  EDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTAL
          EDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTAL
Retrocopy EDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTAL

Parental  PLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTVIEREDGLDGETIFM
          PLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTVIEREDGLDGETIFM
Retrocopy PLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTVIEREDGLDGETIFM

Parental  YMFLAGLGLLVVIGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQETLNQIMQSRRDKASPRRLPRK
          YMFLAGLGLLVVIGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQETLNQI.........PR....K
Retrocopy YMFLAGLGLLVVIGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQETLNQINKA-SPRRLPRKQAQK

Parental  RAQKRSVGSDE
          R....SVGSDE
Retrocopy R----SVGSDE

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_1850 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1850 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850 ,