Sequence
atgc intronic sequence ATGC exonic sequencegtaagttccagcatcgatgataccagttaaaagctttataattatataatccactaagctagctaggaccctataatgtaacttgcgtctgcttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17750.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 5
gtaagttccagcat-cgatgataccagttaaaagctttataattatata-atccactaagctagctaggaccctataatgtaacttg-cgtctgcttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
| |||| | ||| | || || | |||| ||||| | | | | | | ||| | | || | | || | |||| || |||||||||||||||||||||||||| || |||||||||||| | || || || || || || || || || |||| |||||||| | |||||||| ||||
--tgatcttagcaggcaatgtttgcaatttatctatttactgttatacatagagaatgaatatgttagttcatcttgattcaccatggtctatgctctt-cagGTTCTTTTCCAAAATGATTCTCCTGCAACTTTACTTGCACGTGTGATGGGCATCATTGGTTCGATAGAACAAGCTATGCTTGCACAGGGACGTGAAACAT
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 5
gtaagttccagcatcgatgataccagttaaaagctttataattatataatccactaagctagctaggaccctataatgtaac--ttgcgtctgct----tttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
| || | | | || || | ||| || ||| | | || ||| | || | | || | | |||||| || ||| ||||| |||||||||||||||||||| || || |||||||| | || || || || || || || || || |||| |||||||| | ||||| || || |
------ttttttattattatttcaaggtatatattttttacctattttctgtcatatgcttgtatggtgcatggaagctgatgagtgcgtcctctatgcttttcagGTCCTTTTCCAAAATGATTCTCCTGCAACATTACTTGCTCGCGTGATGGGCATCATTGGCTCCATAGAACAAGCTATGCTTGCACAGGGACGCGACACCT
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 5
gtaagttccagcatcgatgataccagttaaaagctttataat-tatataatccactaagctagctaggaccctataatgtaacttgcgtctgc---ttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
| || | | | ||| |||||| | | | | | || || | | | | |||| || | | || | |||| || |||||||||||||| ||||| || |||||||| |||| || |||||||| || ||||||| |||| ||||||| |||| ||| |||||||
----acattgacttcacctcatctactgaaatactttattttctttgttaaatacatgcataattctctcattcttatgtgacacaagaccatgcattatatagGTCCTCTTCCAAAATGATTCCCCGGCAACATTACTTGCTCGGGTGATTGGTATAATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGCACGGGATACAT
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 11
-gtaagtt--ccagcatcgatgataccagttaaaagctttataattatataatccactaagctagctaggaccctata-atgtaacttgcgtctgcttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
| ||| | | | | | | | || | | ||| || ||| | | | | | || || || | |||| | || ||| |||| || |||||||||||||| || || || ||||||||| |||| || || ||||| || ||||||||||||| |||||||| ||||||||||||||||
agcaagatatcttacctggtttaatgtggtcattttccttaaaactatcaattatgattcctggtgcaaagcgctttacataaagtttgc-tatgtttt---agGTCCTCTTCCAAAATGATTCACCAGCGACGTTACTTGCACGGGTGATTGGAATAATAGGTTCAATTGACCAAGGCATGCTTGCTAAAGGACGTGATACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatccactaagctagctaggaccctataatgtaacttgcgtctgcttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
atgtaac putative branch site (score: 3)
tctgctttt putative PPT
tataatgtaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttccagcatcgatgataccagttaaaagctttataattatataatccactaagctagctaggaccctataatgtaacttgcgtctgcttttgcagGTTCTTTTCCAAAATGATTCTCCGGCTACTTTACTTGCAAGGGTCATCGGTATAATCGGATCAATTGACCAAGAAATGCTTGCCAAAGGACGTGATACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA