Sequence
atgc intronic sequence ATGC exonic sequencegttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21180.1 |
intron # | 26 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
------gttagtaccttgatgcttatt--tgaatggttgaacttttaagacaaggataaaagatataatggt---gttctttgat--gcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | ||| || | ||| | | || ||| | | || | | || | | | ||| |||||| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||
gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
-------gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | | | || | | | || | ||| || ||||| |||| ||| || |||| | | ||||| | ||||| ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || | || ||||| ||| | || ||||| |||
ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
----gttagtaccttgatgcttatttgaatggttgaacttttaagac-----aaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
|| || |||| ||| | | || | | | || | | | | ||||| |||| ||| || |||| | | ||||| | ||||||||||||||||||||||| ||||| || |||||||| ||||| || || ||||| || | || ||||| ||| | || ||||| |||
aaaaactaagac--tgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 28
-----------------gttagtaccttgatgc-ttatttgaat----ggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
|| | | || | ||| ||| | | || |||| || | || | | |||| | |||||||||||||||||||| || ||||| || |||||||| ||||| || || ||||| || | |||||||| ||| | || ||||| |||
gtaccctgccctctaatattgttgaatgaatatatgattcaaattacagatagagtcacatttacaatacctgcgtttacccctctcttactgtgtatagCTTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
-----------gttagtaccttg-atgcttatttgaatggttgaactt---------ttaagacaagg-ataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | | || ||| | || ||| || || |||| | | | | | | | | | ||| | ||||| || ||||| ||||||||||||||||||||||||||||||||| | ||||| || |||||||| |||||||||||| | ||| | || ||||| |||
gcagtgtgaaaaatgttgcttttcatggtctttcaaataaccaaatttagggattatttaattcttcttacatcactttttcttttctcacttggtacagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 28
----------------------------------------------------gttagtaccttgat-gcttatttga-atggt----tgaacttttaag--acaaggataaaagatataatggtgttctt-tgatgc----agCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| || ||||| || ||| || |||| ||| |||| ||| | || | || ||| || | | ||| || || | |||||||| | |||||||| ||| | |||||||||||||| ||||| |||||||| || ||| |||||||| || | | || ||||||||||
gtttgtaccttaatctttttaatatgggaaatttagtaacagtgtagtgtcggcgagaaccttaatcatttaactgttatggcgtcatgagattttgcattacataacttaaggttactgatgtgctcatgttgtgctggtagTTGTTATGGGTCAATTTGATCATGGACACTTTGGGAGCACTTGCACTTGCTACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
ctttgat putative branch site (score: 5)
tgttcttt CT-rich tract
ataaaagatataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA