Sequence
atgc intronic sequence ATGC exonic sequencegtacattactaaccatttctttggatttgttatagatcttctccttctctaagactcaataaaaaattgatctttctttggttgcttgtgtatcagCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26180.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G161299_T01 (Zea mays), 3'ss of exon 4
--gtacat-tactaaccatttctttggatttgttatagatcttCTCCTTCTCTAAGACTCAATAAAAAATTGATCTTTCTTTGGTTGCTTGTGTATCAGCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
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gtatgcatgtactg--catctcactgtttttatca-atgccagtttctgatatactcct-ggcaattaactaattttttttt-----------cttcagCTCCTTCACTATATGGAATCTTCCCTTACTCTGGTCTTAAATTCTACTTCTACGAGAAGATGAAGAGCCACGTTCCTGAAGAGCACAGAAAAGGTATCAT
upper sequence: AT4G26180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G161299_T02 (Zea mays), 3'ss of exon 4
--gtacat-tactaaccatttctttggatttgttatagatcttCTCCTTCTCTAAGACTCAATAAAAAATTGATCTTTCTTTGGTTGCTTGTGTATCAGCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
| ||| |||| ||| || || ||| | | | | | || | || || || || | || ||| ||| ||||||||||| || ||||| ||||||||||| ||||| | || ||||||||||||||| ||||||| | || || ||| || || | |||
gtatgcatgtactg--catctcactgtttttatca-atgccagtttctgatatactcct-ggcaattaactaattttttttt-----------cttcagCTCCTTCACTATATGGAATCTTCCCTTACTCTGGTCTTAAATTCTACTTCTACGAGAAGATGAAGAGCCACGTTCCTGAAGAGCACAGAAAAG-------
upper sequence: AT4G26180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G15430.1 (Glycine max), 3'ss of exon 4
gtac-attactaaccatttctttggatttgttatagatcttCTCCTTCTCTAAGACTCAATAAAAAATTGATCTTTCTTTGGTTGCTTGTGTATCAGCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
||| | | | ||||| | | ||||| | | | || ||| | ||| |||| | ||| ||| ||| | || | | ||||||| |||| ||| || ||||| ||||| |||||||| ||||||||||| ||||| ||||| || ||||||||| ||| | || || |||
gtatgacttcaaaccaccttatatcgtttgtatcatactatatcactcttgcattggtaatgcaaaact---cttcattttgtt-catg-gcaacagCTCCAACTCTTGTTGGAATATTCCCATATGCGGGTTTGAAATTCTACTTCTATGAGGAAATGAAGCGCCATGTCCCTGAGGAGTACAATAAAAGCATCAT
upper sequence: AT4G26180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g02470.t01 (Vitis vinifera), 3'ss of exon 4
gtacattactaaccatttctttggatttgttatagatcttCTCCTTCTCTAAGACTCAATAAAAAATTGATCTTTC-TTTGGTTGCTTGTGTATCAGCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
||| | | ||| |||| || |||| || | | || | | | | | | ||| |||| || | |||||||| | |||||||| |||||||| ||| ||||||||||||||||||||||||||||||||||| | ||||| ||| | |||| ||| ||||||| |
gtaggt-attaagtttttccatgtctttgctagttgcttgcaccaagtactatggtaactgtgtctccattaacagatttaaatgct-gt-tctcagCTCCAGCACTCTATGGCATCTTCCCATATTCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAAAGCCATGTGCCTGAGAAACACAAGAAAGACATAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttctctaagactcaataaaaaattgatctttctttggttgcttgtgtatcagCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
aattgat putative branch site (score: 4)
aataaaaaattgatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattactaaccatttctttggatttgttatagatcttctccttctctaagactcaataaaaaattgatctttctttggttgcttgtgtatcagCTCCTTCTCTCTATGGGATCTTCCCTTATGCTGGTTTGAAGTTCTACTTCTACGAGGAGATGAAACGTCATGTCCCTCCGGAACATAAGCAAGACATTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA