Sequence
atgc intronic sequence ATGC exonic sequencegtatggttatcttgatcagagtccaaatttttggtttgaagataaaatttgcaattttgatggtatacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67500.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67500.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G081639_T01 (Zea mays), 3'ss of exon 18
--------gtatggttatcttgatcagagtccaaatttttggtttgaagataaaatttgcaattttgatggtatacagt---------gtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
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ggcagtcctcttacttcccttttgcaacatttgtttttcagttaaaaaaattgttcttaccaattggtggatatattgtaaataattagtttgtttgcagATATTCAATGCACGGCAGCTTGCTTTGAAGCTGATAGCTAATGTCACGTATGGTTACACAGCTGCTGGATTCAGTGGTCGAATGCCTTGTGCAGAGCTTG
upper sequence: AT1G67500.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA03G39720.1 (Glycine max), 3'ss of exon 26
-----------------gtatggttatcttgatcagagtccaa-atttttggtttgaagataaaatttgcaattttgatggtatacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
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ttaattatatctactgtgtgtgatgtagcaaatgattcttttatatgcatgatttaaatatttaaataatatttaccaagtaatacgatttcct-tttcagATATTTAATGCAAGGCAGCTTGCTTTGAAGCTCATAGCGAATGTAACATATGGCTACACTGCTGCTGGATTTAGTGGTCGCATGCCCTGTGCAGAACTTG
upper sequence: AT1G67500.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv14s0128g00840.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtatggttatcttgatcagagtccaaatttttggtttgaag--ataaaatttgcaattttgatggtatacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
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tgtttagattatagtaatatttagactttgttttgaaagaaagaatgcacaaatgtaagccattaaattcactagtttcacaatatc---ttttccctttcagATATTTAATGCAAGACAGCTTGCTTTGAAGCTGATAGCAAATGTAACATATGGTTATACAGCTGCTGGATATAGTGGTCGTATGCCTTGTGCAGAGCTTG
upper sequence: AT1G67500.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S265_31V6.1 (Physcomitrella patens), 3'ss of exon 17
--gtatggtt---atcttgatcagagtccaaatttttggtttg---aagataaaatttgca-attttgatggt--------atacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
||| |||| | || || | |||| | | || || |||| || |||||| | | || || || | ||| | | ||||| |||||| |||| ||||| |||| || |||||||||||||| || || || || || || |||||||||||||| || |||||||| |
gggtaaggttccaagtaacattggatccagaattaggcggacgcacaaattatcattttcatattttggttttcacaatttatttcgtaattttatgcagGTCCTAAATGCTAGGCAGTTTGCGCTAAAGTTGATCGCGAATGTGACTTATGGATACACCGCAGCAGGATTTAGTGGTCGAATGCCATGCGCAGAGCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggtttgaagataaaatttgcaattttgatggtatacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
ttttgat putative branch site (score: 4)
tgtcttctttc putative PPT
ataaaatttgcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggttatcttgatcagagtccaaatttttggtttgaagataaaatttgcaattttgatggtatacagtgtcttctttcagATATTTAATGCGAGGCAGCTTGCTTTAAAGCTGATAGCAAATGTGACTTATGGTTATACTGCTGCTGGCTTCAGTGGTCGAATGCCTTGTGCAGAGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT