Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 2
------gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattg--gcatgaagta--------aaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
|| | | ||| | | |||| ||| | ||| || | ||| ||||| || || || || | |||||||| || ||||| || || || ||||| ||||| ||||||||||| || || |||||||| || || ||||||||||| ||||| ||||| || ||
ctcttagtatttaagactatctgaaaacacttccaaaataaagtatattgtgtacggttgcagcaagtacttgcaatgactagtctttcatattattcagGTTGATCCTGATGAGGTCAATGCGTTGGCACAACTAATGACATGGAAGACGGCCGTGGCTAATATTCCATATGGAGGAGCTAAAGGTGGAATAGGATGCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG----------------------------------------------------
| |||| | || | ||| | || | || | |||||||| || |||||||| || || ||||| ||| | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| || |||
-----------------------------gttggtgaaaaatctggtcctgatgtttg--aaatc---ctttgacaacc--caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 3
gtttgttttactctgttt--ttttttcatcaaaccaaaacaaattcaa---tattggcatgaag--taaaccagatttcggtaatc----gaca-----gGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
| ||| || || |||| | | || || ||| || |||| || | || ||| | | |||| |||| |||||| || |||||||| || || ||||| ||| | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| || |||
atccatttccttcaaattaattttcctcttcatttaagactcattgaaatccgttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccagGTTGATCCTGATGAAGTTAATGCCTTGGCACAATTGATGACTTGGAAAACAGCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagta---------aaccagatttcggtaatc--gacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
||| || || |||| || | | | | | | ||| || | |||| || || || || | |||||||||| |||||||| || |||||||| ||||| ||||||||||| |||||||| || || ||||| ||||| |||||||||||||| || || ||||
gttatttatattctgacttacaaaaaactcagtgatttatctgtt-tataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
----gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaac-------cagatttcggtaatcg-----acagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
| ||||| | | ||| | | | || | || | | ||| || | || ||| | | |||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || || || ||||| ||||| || |||||||||||||| || ||||
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 2
-------gtttgttttactctgt-------ttttttttcatcaaaccaaaacaaattcaatattgg---catgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
||||| || || | ||| | || | | | || || | | | || || | || ||| | ||||||| || |||||||| || ||||| || ||||| ||||||||||||||||| || || || ||||| ||||| || ||||||||||| || || ||||
aactttcgtttgaactagtccctggaactgtttatatttgtatatggtgtgtacttttgattctcagttctcactatgaatcatttaatgg-aataaatagGTTGACCCTGATGAAGTGAATGCTTTAGCACAACTAATGACATGGAAAACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGGATAGGGTGTG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 3
-----------------gtttgttttactctgt-ttttttttcatcaaac-caaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
|| | ||| | | | ||| | || | | |||| || || | || || | || ||| | ||||||| || |||||||| || ||||| || ||||| ||||||||||||||||| || || || ||||| ||||| || ||||||||||| || || ||||
aacttttctgtgaaccagtccctggaactgtttatatttgtatatggtgtgtactttagattctcggttctcactc--tgaatcatttaatgg-aataaatagGTTGACCCTGATGAAGTGAATGCTTTAGCACAACTAATGACATGGAAAACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGGATAGGGTGTG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 4
-------gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcg----------acagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
|| | | || | || | | ||| || ||| | | | ||| | | |||| ||||||| || ||||| ||||| |||||||| ||||| ||||| ||||| |||||||| || || || || || || || ||||||||||| || || |||
ccagggttttcatgtagctttaaattaaatctactct-ccagcttgggaacagatttgtgctattgcagtttcagtttggatgatcgcatagcttttgtagGTTGACCCAGATGAGGTAAATGCTTTGGCACAACTAATGACGTGGAAGACAGCAGTAGCAAATATTCCATACGGTGGGGCCAAAGGAGGGATAGGATGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
aaacaaattcaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA