Sequence
atgc intronic sequence ATGC exonic sequencegtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26840.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
-gtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgt--tattttagaggctttaatgaaca--aacaa------aatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
||| || | | | ||||| || | | | | | || ||| ||| |||| | || | | | |||| |||| |||||||||||||||||| | || ||||| |||| ||||||||||| || | ||| | | ||||||||||||||| || ||||||||||| ||||||||||
tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
----------gtgatatatagtttgta-aactttttccgggtttctgcattcttg-aaacttgt-tattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
| | | | ||| | || | || | ||| ||| || | ||| | || |||| | ||| | || || ||| |||||||||||||||||| | || ||||| ||| || |||||||| || | ||| | | |||||||||||||||||| |||||||||| ||||||||||
ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataa--ttttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 3'ss of exon 10
---------gtg-atatatagtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatt-tgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
||| || |||| || || | | | | | || || || || || | || | ||| | ||||||| ||||||||| ||||||||||||||| || |||||||| || |||| ||| ||||||||||||||| | || ||||| |||||||||||||
aaaatatgtgtgcatgtatatttcatagccatgaagtagacatgtcggggtcacaattttaaaataccttttgcaatactcaattgttcatattgtttagGGTGAGGAATACAAGTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAG
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
------------------------------------------------------------------------------------------------------gtgatatata-gtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatg-aacaaacaa--------aatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
||| |||| || || | | | | | ||| ||| || ||| | ||| | |||| || |||| ||| | | | |||||||| ||||||||| |||||||||||||| || |||||| | || | || ||| |||||||||||||||||| || ||||| || ||||||||||
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgc---cttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ23061 (Selaginella moellendorffii), 3'ss of exon 10
gtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
| || | || ||| || | || | ||| | || ||||| || ||||||||||| ||||||||||||| |||||||||||| || | || | || || |||| || ||||||| | ||||| ||||
-------------------------------gtatg-gtatttatctcttcttttctttgtcaacttaccatctggatttttttcccagGGAGAGGAATACAAGCTCTTTTGGCCAGAACAGTCCGAGTTTGTCCGAATGGCTGCGCGTTTCGGTGCCACCATAATTCCTTTCAGCTGCGTTGGCGAAG
upper sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ30477 (Selaginella moellendorffii), 3'ss of exon 10
gtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
| || | || ||| || | || | ||| | || ||||| || ||||||||||| ||||||||||||| |||||||||||| ||| | || || || || |||| || ||||||| | ||||| ||||
-------------------------------gtatg-gtatttatctcttcttttctttgtcaacttaccatctggatttttttcccagGGAGAGGAATACAAGCTCTTTTGGCCAGAACAGTCCGAGTTTGTCAGAATGGCTGCTCGTTTCGGTGCCACCATAATTCCTTTCAGCTGCGTTGGCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
ctttaat putative branch site (score: 4)
tttaatgaacaaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA