RetrogeneDB ID: retro_itri_1722

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393665.1:689511..690141(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM168A
• Ensembl ID: ENSSTOG00000014507
• Aliases: None
• Description: family with sequence similarity 168, member A [Source:HGNC Symbol;Acc:28999]

Sequence

>retro_itri_1722
CCTACAGCCTACCCGGCAGCGGCACCTGCCTACAATCCTAGCCTGTACCCAACCAATAGCCCCAGTTATGCTCCAGCCAC
TCTGCTGATGAAACAGGCCTGGCCACAGAACTCGTCTTCCTGTGGCACTGAAGGCACCTTCCACCTCCCAGTGGACACCA
GGACCGAGAACCGAACTTACCAAGCATCCTCTGCGGCTTTCAGATATACTGCAGGGACTCCATACAAGGTTCCACCAACC
CAGAGTAATACTGCTCCAACCCCCTACTCCCCATCACCCAACACCTATCAGACAGCCATGTATCCAATCAGAAGTGCCTA
CCCCCAGCAGAATCTGTATGCACAGGGAGCCTACTATACACAGCCGGTGTACGCTGCCCAGCCCCATGTCATCCACCATA
CCACGGTCGTCCAGCCTTACAGCATTCCCTCTGCCATCTACCCGGCGCCTGTTGCTGCCCCCAGGACCAATGGCATGGCC
ATGGGCATGGTGGACGGCACCACCATGGCAATGTCAGCAGGTACTCTGCTGACTACACCCCAGCACACCGCGATTGGGGC
ACACCCTGTCTCCATGCCAACATACAGGGCCCAAGGAACCCCTGCGAACAGCTACGTGCCCCCGCACTGG

Alignment

ORF - retro_itri_1722 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 84.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSLYPTNSPSYAPEFQFLHS---AYATLLMKQAWPQNSSSCGTEGTFHLPVDTGTENRTYQASSAAFRYT
          P..YP...P.Y.P......S...A.ATLLMKQAWPQNSSSCGTEGTFHLPVDT.TENRTYQASSAAFRYT
Retrocopy PTAYPAAAPAYNPSLYPTNSPSYAPATLLMKQAWPQNSSSCGTEGTFHLPVDTRTENRTYQASSAAFRYT

Parental  AGTPYKVPPTQSNTAPPPYSPSPNPYQTAMYPIRSAYPQQNLYAQGAYYTQPVYAAQPHVIHHTTVVQPN
          AGTPYKVPPTQSNTAP.PYSPSPN.YQTAMYPIRSAYPQQNLYAQGAYYTQPVYAAQPHVIHHTTVVQP.
Retrocopy AGTPYKVPPTQSNTAPTPYSPSPNTYQTAMYPIRSAYPQQNLYAQGAYYTQPVYAAQPHVIHHTTVVQPY

Parental  SIPSAIYPAPVAAPRTNGVAMGMVAGTTMAMSAGTLLTTPQHTAIGAHPVSMPTYRAQGTPAYSYVPPHW
          SIPSAIYPAPVAAPRTNG.AMGMV.GTTMAMSAGTLLTTPQHTAIGAHPVSMPTYRAQGTPA.SYVPPHW
Retrocopy SIPSAIYPAPVAAPRTNGMAMGMVDGTTMAMSAGTLLTTPQHTAIGAHPVSMPTYRAQGTPANSYVPPHW

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_1722 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1722 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016497	1 retrocopy	retro_btau_1748,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262,
Ictidomys tridecemlineatus	ENSSTOG00000014507	1 retrocopy	retro_itri_1722 ,