Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
-----gtaagtttgtgctttgtcgtttttgt-gtgcttgtttggtttctctgcgtaattttg---ggtataatttg--gaattggttgatg----tgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
| | | | ||||| | | || | | || | | | | | | ||| |||||| | |||| || | |||||| |||||||| || || |||||||| ||||| ||||||||||||||||| | | |||||| |||||||||||||||||||| |||||||| ||||||
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
--gtaagtttgtgctttgtcgttttt--------gtgtgcttgtttg-gtttctctgcgtaattttgggta-taatttggaatt---ggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
| | |||| | || |||| || ||| || | | | | ||| ||||| | | ||| |||||||| |||||||| || || |||||||| || || |||||||| || ||||| | | |||||| ||||||||||| ||||||| || | || || |||
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G116506_T01 (Zea mays), 3'ss of exon 1
gtaagtttgtgctttgtcgtttttgtgtgcttgt--ttggtttctctgcgtaat----tttgggtataatttgg-aatt----------ggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
| ||| || |||| || | | | | | | | |||| | | || |||||| | | |||| ||| |||||| | |||||||| || || |||||||| || || ||||||||||||| ||| | | |||||| || |||||||| |||||||| || | || ||||||
--actgatgttctcccacgttcttttatcccagaaatggaactatctgtgcgttgatattctactataatgtagtaattccctacttcacattgtgttgtagGTTTGAGCAAGAGTCGGGGTTCTTCTTCAATATGAAGTACTTTGAAGCGAAGGGCCATGCTGGGGACTGGGATGAGGTGGAGAAATACTTGTCAGGTTTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
||| | |||| | | | | | | ||| | ||| | || || | | ||||| ||||||||||||||||||| ||| ||||| |||||||||||||| | | | ||| |||||||| || ||||||| ||| | ||||| |||
------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgtgatt--ttggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
||| | |||| | | | | | | ||| | ||| | || || | | ||||| ||||||||||||||||||||||| ||||| |||||| ||||||| | | | ||| |||||||| || ||||||| ||| | ||||| |||
------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgatt--ttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
||| | |||| | | | | | | ||| | ||| | | || || | | ||||| ||||||||||||||||||||||| ||||| |||||| ||||||| | | | ||| |||||||| || ||||||| ||| | ||||| |||
------------------------gtgaggagatttgtggtttgttcttgttggtggatgtaagtgttatgtgatt--ttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
||| | |||| | | | | | | ||| | ||| | | || | | ||||| ||||||||||||||||||| ||| ||||| |||||||||||||| | | | ||| |||||||| || ||||||| ||| | ||||| |||
------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgcgatt--ttggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
ggttgat putative branch site (score: 5)
tataatttggaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT