Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36070.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
---------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtaga--taatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
| | | | | | | || || | | | || | |||| || | | ||| | | |||| | |||| || || || ||||| || ||||| || ||||| |||||| | || |||| |||||| || ||||| ||||||||||||||||| ||
aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 5
--------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagata-atggaggtgattttg-tgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
||||| | ||| || | | | | | | || | | | | ||| | ||| |||| | |||| | || || || ||||| || |||||||| ||||| ||||| | ||||| |||||||| || ||||| || ||||||||||| |||||
gtgcatgcatgcacatgtttttaacttaatgttctgtagttttccctgtttgacttttgcagtatgtgttagttataggttacacttaactattgttgcttgcaatcacagGGAGGCAATTCCGTGACATTGTTGGAAGTGCCTACTACGTAGCACCAGAAGTACTCAAACGCAGGTCAGGGCCAGAATCCGATGTTTGGAGTATAGGTGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
| | || | || ||||| | || | || | || | || | |||| |||||| || ||||| ||||| || || || || ||||| ||||||||||||||||| ||||| | |||||| ||| ||||||| || ||||||||||||||
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataa---tggaggtgattttgtgaaaatg-gcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
| || | || ||| | | || | || | || |||| | | |||| |||| |||||| || ||||| ||||| || || || || ||||| ||||||||||||||||| ||||||| ||| || ||| ||||||| || ||||||||||||||
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcagg-catgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 6
---------------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataatggaggtgatt--ttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
|| | | | |||| ||| | || | | || | | |||| | | ||| || | ||||| || ||||| ||||| || || || || ||||| |||||||| |||||||| ||||||| |||||| || || || || || ||||||||||||||
gtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaa--tgttcttgcaatctttatt-tgagttatggttttctctctttgcaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGTAAGTCAGGTCCCGAGTCGGATGTATGGAGTATTGGTGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
------------------------------------gtaaaagtttcacttgtca--agtcttgtccctgagagcagaa--tggtagataatggaggtgattttgtgaaaatg--gcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
| | | ||| || | ||| | || | | | || || || | | | | | |||||| ||||| || ||||| ||||| || || || || ||||| |||||||| |||||||| ||||| | |||||| || || ||||| || ||||||||||||||
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------gtaaaagtttcacttgt-----caagtcttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
| ||||| |||| ||| | || || | | | | ||| | || ||| |||| ||| ||||| ||||| || || || || ||||| ||||| |||||||| |||| ||| | || |||||||||||||| || ||||||||||||||
gtaagtgaaatttcgccttctcaatatatggactttgaaatccatattttcatgggtttctgttgttcaaacaattacaacatatgcttctagcttttgaattggaaaaactgaatatgaataaaca-cagGGAAGAAGTTTCAAGATATTGTTGGTAGTGCCTACTATGTTGCTCCTGAAGTATTGAGACGGAAATCGGGACCTGAATCAGATGTCTGGAGTATTGGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
tagataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG