Sequence
atgc intronic sequence ATGC exonic sequencegtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14350.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 2
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttt-tttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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------------------------------------------------------------------------------------gattttttcccccatatcttgctgcataaataactctgatttttcataaagatatttatcagatgatttgttgcaattttgcaattctttcttttcatagGTTAGAATCTGCCGGGAGAAGGCCACTGGCCATGTTTATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGAAGAGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 2
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcat-gcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcat-gctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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--------------------------------------------------------gtatagtataatctacctttattttcattgaagt-taaaaaaaaaactatgcttctgatctttcacatatgttacaaa-aattgttagataatttgcaactttgcaaattttcttcttcttttgtatagGTCAGAGTCTGCCGAGAGAAAGCAACCGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 2
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagt-atggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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------------------------------------------------------------gtatagtctgcctttattttcattgaagt----taaaaaaaaactatgcttctgatctttcacatatgttacaaaaattgtcagataatttgcaactttgcaattttttccttt---tttatagGTCAGAGTCTGCCGAGAGAAAACAACTGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 3
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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-----------------------------------------------------------------------------tttttccaatatatatatat------gtcttgctgcataaccagatttctcataaagatatttatcagatgatttgttacaattttgcaattctttcttttcatagGTTAGAATCTGCCGGGAGAAGGCCACTGGTCATGTATATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGTAGAGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 2
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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------------------------------------------------------------------------------gtttgtggaaaat--tttctgcactgtctgttttctttgatgctgttataacatttcatttaacttgattgcaccccttgtt---cttacttttctgttctgtagGTTAGAGTCTGCAGGGAGAAGAAAACCGGCCATGTATATGCCATGAAGAAGCTTAAGAAATCAGAGATGCTTCGAAGGGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
||||| | || |||| | ||| || | | ||| | || || | ||| | | ||| | | || | | | | | | | | ||||| ||| | || | ||||| || | ||| ||||| ||||||||||| ||||| || ||||||||||| |||||||||
---------------------------------------------------------------------tgaaacctact-------gcatttctgttgtaa---catgcgaggtgtcatggatt--caggggcaatgtcggtgctaggtaagata-acttgtgtctattatgcacgct-cagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 2
----gtaacatc--tct---tttatagatcatagtctgttactctgttttctcagcctctcattggca---tgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaattt----ttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
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gtatgtgtccttagtctgaatctgcattccatattcgactagtttgtttaaatgcacttgaatttgctaaccgtgccaagttcggtcatacttccggttatatgctgtgtg----ccttttctagcatgtgaaaatgtatttgattaagacatcggggatttgatattagctaatttaagctgatgttgcatgtgacagGTGAGGTTGTGCAGAGAGAAAACAAGTTCTACAGTCTATGCCATGAAAAAACTGAAGAAGTCTGAGATGCTTCGAAGAGGCCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47828550|gb|CK118234.1|CK118234EST: CTGATGACTTTGAGCCATTGACAATGATTGGGAAGGGTGCATTCGGAGAG GTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAG
genomic: CTGATGACTTTGAGCCATTGACAATGATTGGGAAGGGTGCATTCGGAGAGgtaacatctc ... ctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
tgctaat putative branch site (score: 2)
tgctaatttttctctt CT-rich tract
taatttttcaaaaaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG