Sequence
atgc intronic sequence ATGC exonic sequencegtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
||| | || | | |||| | | || | | || || || || || || | | | | || | | || |||| | ||| || || | |||||||| ||||| || | || || | ||||| || || ||||| ||||||||||| ||||||||||||||||| || ||||||
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccg-tgatcgattgtcttccgtttgtcttactgcctcgtctgc-gtcta---------aaactttacct------gcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
| | || | | | | | | | ||| || | | | | | |||| | || | |||| | | | | || || ||| | | |||||| || |||||||| | || || || || ||||| ||||||| |||||||| ||||| |||||||||||||| || ||||||
------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcg-----------aatgaat-cgaattgacttctgcgcctggttgg-gttgcctgtgcttgttgctcc--tgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 2
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG-----------------
| | || | | | | | | | ||| || | | | | | |||| | || | |||| | | | | || || ||| | | |||||| || |||||||| | || || || || ||||| ||||||| |||||||| ||||| |||||||||||||| || ||||||
------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcg-----------aatgaat-cgaattgacttctgcgcctggttgg-gttgcctgtgcttgttgctcc--tgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAGGTCGGCAATGGGTGTCT
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
| | |||||| | | || | || | ||| | ||| | | || ||| | || | | || | || || || ||| || | || |||||||||||| ||||| || ||||| || ||||| | || ||||| ||||||||||| ||||||||||| || ||||| || |||
-------------------------------tctgttttttctctcaattttcttcttttgt-caaaagcata-aaaaattggaaagaaatattaacaaaataagat--atttatgtgttttattgttga-tgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 2
gtatgccctatcacct-tctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
| || | | |||||| |||| || ||||| || || || | |||| | | ||| || || || |||| |||| ||| | ||| | ||| | |||||||||| ||||| || ||||| || ||||| | || ||||| ||||||||||| ||||||||||| || ||||| || |||
------------atctgtttttactctcaattttcttctttttatc-------aaaatcataaaaaatagga----aagaaattaacaaaat--------aaga-tatttatgtgt---tttattgttg--acacagTTAGTGTAAGTGAGATTGAAGCACTGTATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
||||||| |||||||||||||| |||||||| || |||||||| ||||||||||| || ||||||||||| || || ||||||
----------------------------------------------------------------------------------------------------------------------------------------ttAGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 1
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
| || | | | | | | | || ||| | | ||| | ||| ||| || | ||||||| | | ||| ||| ||| ||| |||||||||| |||||||| || || || || ||||| |||||||| |||||||| || ||||||||||| || || || ||||||
----------------------------tcattcctacctaatgctaatagtttgctttc-tgccaactcttttaatgaaccattaaagcattgtactgaagatt----gtaatt---tttttctttccaatacagTTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
tattgat putative branch site (score: 3)
aatatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA