Sequence
atgc intronic sequence ATGC exonic sequencegtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
| | || | || | || | | | || || || || |||| | | | || || | || ||| ||||||| ||||| || ||||| | |||||| |||||||||||||| |||| ||| |||||||| || || | || || || |||||
gtaatcactctctgcctattatagacttttgcatcacaaaatactttgtttgtttcagctcatttatctcatagcttattcttatgcattacttgtcattatattgtgacagatgaactgtattatttattcttgttatttatttttattactaactgttgtttttgttgatggaatgttttcagAGAGTTGCATTATCTACAGCTGCTAATATGTGTAGGAAACTTCCTTCTGATGCATCAGATTTTGTAATGGAAGCGGTTCCACTTCTTACTAATCTACTGA
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttact---cgtgtatcta-atgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
||| || | | | | | | | | ||| | | || | | ||| | ||| | || || |||| || ||| | ||||||||||| || ||||||||||| || ||||| |||||| |||||| ||| ||||||||||| ||| | ||||||||||| ||||
gtaaattgtcagtgaagtacctaaatttagaggatgattatattatatggtccttttggatagtcataaatcatttggccacagatgcctttagtgagcaagtgtgtgtatgttgacattattc--tttgtttcagCGGGTTGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTTCAGATGCAGCTGATTTTGTGATGGAAGCTGTTCCTCTTCTGACAAACCTTCTTC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
||| | | | | | | | | | ||| | | ||| | ||| | || || |||| || ||| | ||||||||||| || |||||||| || || ||||| |||||| |||||| ||| ||||||||||| ||| | ||||||||||| ||||
gtaaattgtcagtgaagtacctacatttagaggatgattgcatcccactggtccttttggacagtcataaatcatttggccacaggtgccattagtgagcaagtgtatgttgacattattc--tttgtttcagCGGGTTGCATTGTCTACTGCTGCAAATATGTGCAAAAAGCTTCCTTCAGATGCAGCTGATTTTGTGATGGAAGCTGTTCCTCTTCTGACAAACCTTCTTC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 2
-------gtgggtaaatttctaacttc---------tcttttatgctacactt---actcgtgtatctaatgcacatgtt-acttggct-tcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
| | || | |||| || | || || | || || || | || | | || || || || | || |||| || ||| | ||||||||||| || ||||||||||| || ||| |||||||| |||| | ||| ||||||||||| || | |||||||||| ||||
gtaactcatcaatgaaatcctaatatcaaagggtgatgattcattttgcatttgccacccttgattggcaagcctatattgacacaatcatgtttcagCGGGTGGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTCCTGATGCAGCTGACTTTGTGATGGAAGCTGTTCCACTTTTGACAAACCTCCTTC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 2
-------gtgggtaaatttctaacttc---------tcttttatgctacacttact---cgtgtatctaatgcacatgtt-acttggct---tcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
| | || | ||||| || || || | | |||| | || | | || || || || | | || |||| || ||| | ||||||||||| || ||||||||||| || ||| |||||||| |||| | ||| ||||||||||| || | |||||||||| ||||
gtaactaatcaatgaaatcctaacatcaaagggtgacaattcattttgcgtttaccacccttgattagcaagcctatattgacataatcatgtgtttcagCGGGTGGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTCCTGATGCAGCTGACTTTGTGATGGAAGCTGTTCCACTTTTGACAAACCTCCTTC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
| ||| | | | || || | |||| || | || ||| | || | | | ||||| || || |||| || || | ||||| ||||| || |||||||||||||| ||||| |||||| |||| | ||| ||||||||||| ||| || |||| ||||| || |
gtaaatcgccattaaaatttgtgtgtgtatattctttttaacctttttgttgattatgcacgctgagggaagaatactgttttatattttgtg----gggtcatcaagtaatttat-ctccttttact--atttgtttcagCGAGTGGCCTTGTCTACAGCTGCAAATATGTGCAAGAAACTCCCTTCAGATGCAGCTGACTTTGTGATGGAAGCTGTCCCTCTGTTGACGAACCTTCTGC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
||| | | | | || || | | || | | | | | | ||| || | || || | |||||| | || ||||||||||| ||||| |||||||| ||| | |||||| | || | ||| ||||||||||| ||| | |||||||||| ||||
gtaaaattttggctatttactcgtatgctgtgctccttggtcttctggggc-catattgggatttttctgaagaagtttatttccatgttttcagAGAGTAGCATTGTCCACTGCTGCCAATATGTGTAAGAAACTCCCTCCAGATGCAGCCGACTTTGTGATGGAAGCTGTGCCTCTTTTGACAAACCTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
cttcttgt CT-rich tract
tatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG