RetrogeneDB ID: retro_itri_1872

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394303.1:15926..17475(+)
• Located in intron of: ENSSTOG00000001840

Retrocopy information

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

Parental gene information

• Parental gene symbol: SACM1L
• Ensembl ID: ENSSTOG00000014779
• Aliases: None
• Description: SAC1 suppressor of actin mutations 1-like (yeast) [Source:HGNC Symbol;Acc:17059]

Sequence

>retro_itri_1872
GTAATTATCTTATCATCATTACCCAAAATACAAAAATAGGTGAATTTTTTAATCATGTAATCTGGAAAGCATGATATCCT
TTCTTATAAGAAGATAATGTTGCACTTAACTGATATTTAGTTACAAGATAATAAAACTTTCGTTTTGATGCTAAACCATG
TCTTGAGTGTGGATGGGTTTTACTTATCAACAACATATGATTTGACCCATACTTTGCAGCAGTTGTCCAACACTAGTACA
GAATTGCAAGAAATGAGTCTCTTGGAACGGGCAGATCAGCGATTTGTATGGAATGGTCATCTTCTAAGAGAACTGTCTGC
TTAGCCTGAGGTTCATCGTTTTGCTCTTCCAGTGTCACATGGTTTTTATTACTATACACTCATGTTCTATCAATGGAAAA
TACTTCAATTGGATTCTCATTTCCAGGAGGAGTTGTTTCAGAGCTGGCGTGGATTATTATGTAAGAGGAATTGATTCTGA
AGGCCATGCAGCTAACTTTGTAGAAACAGAACAAATTGTGCACTATAATGGGTGCAAGGCTTCATTTGTACAGACTCGAG
GATCAATCCCTGTCTTCCGGTCCCAAAGACCAAACCTCAAGTATAATCCATGACCCCAGATCAACAAAGAAGCAAATTAT
ATGGATGGTTTCCAAAGCATTTTGATTCACAAGTAATTATTTATGGAAAACAAGTCATAATCAATCTGGTAAACCAGAAG
GGCTCAGAGAAACCACTTGAACAAACATATGCAAGAATGGTGTCTTCCTTGGGAAGTGGAATGATCAGATACATTGCCTT
TGACTTCCATAAGGTATGTAAAAATATGAGATGGGATCAACTAAGTATTTTATTGGATCAGGTATCAGAAATTCAAGATG
AATTAAGTTATTTTCTAGTAGACTCTGCCGGCAAAGTGGTGACAAACCAGGAAGATGTGTTCCCCAGCAATTGTATGGAT
TGTCTAGGATAGAACCAATGTGATCCTGAGTTTGTTAGCTCATCGGTCTCTTCAGGCCCAGCTTCAGAGACCAGGTGCTT
TGTATGTGGGACAAAAGCTTGAAGAACAAGAGGAATTTCAGAAGATCTATAAAAATGTCTGGGCTGACAAAGCAAATGCT
TGTGCCAAACAATATGCTGGAACCAGTACCTTGAAGACTGGCTTTACCAGAACTGAGAAGAGAACTCAGTTAGTTCTCAT
AAGGAATGGTTGGAACTCACTCAAATGATATTACAAGATCAACTTTTCTGATGGACTTAGACAGGATTCCATAGACTTAT
TTCTTGGGAACTATTTAGTGGATGAATTAGAATCTCATAGTCCTTTAAGTGTTCCAAGGGACTGGAAATTCCAGGCTTTG
CCTATTATTATGGTTGTTGTCTTTTCAATGTGTATTATCTGTTTGCTTATGGCTGGTGACACTTGGACAGAAACACTGGC
TTATGTACTTTTCTGGGGAGCTGCAAGCATTGGAACATTTTTTATTATTTTTTACAATGGCAAAGATTTTGTTGATACTC
CTAGATTGGTCCAGAAAGAAAAGATAGAC

Alignment

ORF - retro_itri_1872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.36 %
• Parental protein coverage: 88.51 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIVITKKTKIGEFFNHVIWRATDFDVLSYKKTMLHLTDIQLQDNKTFLSMLNHVLSVDGFYFSTTYDLTH
          .I......KI....N..I......D.LSYKK.MLHLTDI.LQDNKTF..MLNHVLSVDGFY.STTYDLTH
Retrocopy VIILSSLPKIQK*VNFLIM*SGKHDILSYKKIMLHLTDI*LQDNKTFVLMLNHVLSVDGFYLSTTYDLTH

Parental  TLQRLSNTSPEFQEMSLLERADQRFVWNGHLLRELSAQPEVHRFALPVLHGF-ITMHSCSINGKYFNWIL
          TLQ.LSNTS.E.QEMSLLERADQRFVWNGHLLRELSA.PEVHRFALPV.HGF.IT.HSCSINGKYFNWIL
Retrocopy TLQQLSNTSTELQEMSLLERADQRFVWNGHLLRELSA*PEVHRFALPVSHGF>ITIHSCSINGKYFNWIL

Parental  ISRRSCFRAGVRYYVRGIDSEGHAANFVETEQIVHYNGSRASFVQTRGSIPVFWSQRPNLKYKPRPQINK
          ISRRSCFRAGV.YYVRGIDSEGHAANFVETEQIVHYNG..ASFVQTRGSIPVF.SQRPNLKY.P.PQINK
Retrocopy ISRRSCFRAGVDYYVRGIDSEGHAANFVETEQIVHYNGCKASFVQTRGSIPVFRSQRPNLKYNP*PQINK

Parental  VANHMDGFQ-RHFDSQVIIYGKQVIINLVNQKGSEKPLEQTFATMVSSLGSGMIRYIAFDFHKECKNMRW
          .AN.MDGFQ..HFDSQVIIYGKQVIINLVNQKGSEKPLEQT.A.MVSSLGSGMIRYIAFDFHK.CKNMRW
Retrocopy EANYMDGFQ<KHFDSQVIIYGKQVIINLVNQKGSEKPLEQTYARMVSSLGSGMIRYIAFDFHKVCKNMRW

Parental  DRLSILLDQVAEIQDELSYFLVDSAGKVVTNQEGVFRSNCMDCL-DRTNVIQSLLARRSLQAQLQRLGVL
          D.LSILLDQV.EIQDELSYFLVDSAGKVVTNQE.VF.SNCMDCL.DRTNVI.SLLA.RSLQAQLQR.G.L
Retrocopy DQLSILLDQVSEIQDELSYFLVDSAGKVVTNQEDVFPSNCMDCL>DRTNVILSLLAHRSLQAQLQRPGAL

Parental  HVGQKLEEQDEFEKIYKNAWADNANACAKQYAGTGALKTDFTRTGKRTQLGLIMDGWNSLKRYYKNNFSD
          .VGQKLEEQ.EF.KIYKN.WAD.ANACAKQYAGT..LKT.FTRT.KRTQL.LI..GWNSLK.YYK.NFSD
Retrocopy YVGQKLEEQEEFQKIYKNVWADKANACAKQYAGTSTLKTGFTRTEKRTQLVLIRNGWNSLK*YYKINFSD

Parental  GFRQDSIDLFLGNYSVDELESHSPLSVPKDWKFLALPIIMVVAFSMCIICLLMAGDTWTETLAYVLFWGV
          G.RQDSIDLFLGNY.VDELESHSPLSVP.DWKF.ALPIIMVV.FSMCIICLLMAGDTWTETLAYVLFWG.
Retrocopy GLRQDSIDLFLGNYLVDELESHSPLSVPRDWKFQALPIIMVVVFSMCIICLLMAGDTWTETLAYVLFWGA

Parental  ASIGTFFIILYNGKDFVDAPRLVQKEKID
          ASIGTFFII.YNGKDFVD.PRLVQKEKID
Retrocopy ASIGTFFIIFYNGKDFVDTPRLVQKEKID

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_1872 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1872 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000014779	2 retrocopies	retro_itri_1642, retro_itri_1872 ,