Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttttgcatttcccaaagcgccaactactacaaatttaattgcttcggtttgctaacatgttattccttttcgtagGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28080.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os02g15660.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gtatgctttttgcatttcc---caaagcgccaactactacaaatttaattgcttcggt--ttgctaacatgttat--tccttttcgt-----agGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
|| |||| ||| || || | ||||| | ||| || | | | ||||||| || ||| || |||||||| || |||||| | ||||||||||| || ||||||||||| || ||||| ||||| ||||| |||||||| || || |||||||||||||||||
gtatgtgcttgttgtcgtttacaaaagctatatgcctagggtgccatctagtttgtttttatgagtaagctatgaagtctgttctatttactctctttggaaatctcaactatgttatgctctgttttgtgtatcagGTATGTGAATCGTGCCCTATATCTTTTGCACCTGACATGTGGACCCTCTCATCCTAATACTGCTGCAACTTATATTAATGTGGCAATGATGGAAGAAGGG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 18
---------------------------------------------------------gtatgctttttgcatttcccaaagcgccaactac---tacaaatttaa---ttgcttcggtttgctaacatgttattcctttt--cgtagGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
||| || || || | || | | ||| ||| | ||| ||| | | | | || | ||||||||||| |||||| | ||||||||||| || |||||||| || || ||||| || || ||||| |||||||| || || || ||||||||||||||
gtaagttcagagtcatctacttaagctgacatggtaaaaatggacgacactatagttttatttcttcccacttacctgtggagcttgtttcatttaccgttttcatgtttgaactactttatttatgttctgactgttatatttcagGTATGTCAATCGTGCCCTATATCTTTTGCACCTTACATGTGGCCCTTCTCATCCTAACACCGCTGCAACTTATATCAATGTTGCGATGATGGAAGAAGGG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 15
-----------gtatgctttttgcatttcccaa--agcgccaactactacaaatttaat-tgcttcggtttgctaacatgttattccttttcgta----gGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
||| ||||| ||| | | | | | | || ||| | | || | | ||| | || | | || ||| ||||||| || ||||| ||||||||| |||| |||| |||||||| ||||||||||| || |||||||| ||||| || || |||||||||||||||||
gttcaagttttgtaatatttttcatttttctagttattgtaacgcattagaaaaatcctgtgaataattacattaatctttttaccttatttgtatctagGTATGTTAATCGTGCTTTGTATCTTCTGCACTTAACCTGTGGACCTTCACATCCAAACACTGCTGCCACCTATATTAATGTTGCAATGATGGAAGAAGGA
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 16
---------gta-tgctttttgcatttc---ccaaagcgccaactactacaaa-tttaattgcttcggtttgctaacatgttattccttttcgta----gGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
||| | |||| |||| | | | | | | | ||| | ||| | | ||| | || || | || ||| ||||||| || ||||| ||||||||| |||| |||| |||||||||||||||||||| || |||||||| || || || || |||||||||||||||||
tggggtttagtaatatttttcatttttctagctatatcataagacataagaaaactcctttgaataattacattaatttttttatcttatttgtatctagGTATGTTAATCGTGCTTTGTATCTTCTGCACTTAACCTGTGGACCATCACATCCAAACACGGCTGCCACCTACATTAATGTTGCAATGATGGAAGAAGGA
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 18
-------------------gtatgctttttgcatttcccaaagcgccaactactacaaatttaattgcttcggtttgctaacatgttattccttttcgtagGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
| |||| | | | | | | || | | || | | | ||| || |||||||| |||||||||||| ||||| || |||||||||||||| ||||| || ||
agacccatcaaaaaaaaaaaaaaagttttaacctgctctgagataatgatttctgtatgatcaaagatatgcatcttacttcatctt-ttcctttttctagGTATGTCAATCGTGCATTATATCTTTTGCATCTTACATGCGGGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 18
gtatgctttttgcatttcccaaagcgccaactactacaaatttaattgcttcggtttgctaacatgttattccttttcgt-agGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
||| || | || || || | ||| | || || || || || || || | || | |||| | | |||||||| |||||||| ||||||||||| ||||||||||| ||||| |||||||| || | |
-----------------------------------gtaaagttgctcttttaagtagtgtactctattaacttctgaggtcagATACGTTAATCGGGCACTTTACTTGCTGCACTTGATCTGTGGACCCTCACATCCGAATACAGCTGCTACTTATATAAATGTAGCTATGATGGAGGAGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactactacaaatttaattgcttcggtttgctaacatgttattccttttcgtagGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
tgctaac putative branch site (score: 1)
tgttattccttttc CT-rich tract
actacaaatttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttttgcatttcccaaagcgccaactactacaaatttaattgcttcggtttgctaacatgttattccttttcgtagGTATGTCAACCGTGCCTTGTATCTTTTGCATCTAACATGTGGACCATCACATCCAAATACAGCTGCCACTTATATAAACGTAGCAATGATGGAAGAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG