Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttatctccttacaagctctagagtctatcttctctccctgtgtggaacacaatgtgtatgaacagataaatagatagagatttgtgacggaaattgcttataaagatatccgtttctcttttccttctagACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48960.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 13
gtttgtttatctccttacaagctctagagtctatcttctctccctgtgtggaacacaatgtgtatgaacag-ataaatagatagagatttgtgacggaaattgcttataaagatatccgtttctcttttccttcta-gACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
| | | | | | | || | || || | ||| || | | | ||| | | || || | | || ||||| | ||| | | ||| || || || || || |||||||| |||| || || || | |||||||||||| |||||||| ||||||||||| ||||| || |||| || |||||
-------------------------------tttttattataattttttgaagttatccagataagactattatatattattggcgtattgctttag----tactgattgaaagat---tttctgtgttcttaaaaagACCCTAGCAGCAACTAATCTGGATGATGAAGACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGC
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 13
gtttgtttatctccttacaagctctagagtctatcttctctccctgtgtggaacacaatgtgtatgaacagataaatagatagagatttgtgacggaaattgcttataaagatatccgtttctcttttccttctagACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
|| | | | | | | | | || || | ||| || | | ||| | | | || || ||| ||| |||| | ||| | |||| || || || || |||||| ||||| |||| || || || | |||||||||||| |||||||| ||||||||||| ||||| || |||| || |||||
-----------------------------actttttattatattttttttaagttacccagataagactatatacattattggcctattgcttcagta-ctgattgtaa-gat-----tttccatgttcttaaaagACCCTAGCAGCAACTAACTTGAATGATGAAGACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGC
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 13
gtttgtttatctccttacaagctctagagtctatcttctctccctgtgtggaacacaatgtgtatgaacagataaatagatagagatttgtgacggaaattgcttataaagatatccgtttctcttttccttctagACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
|| | | || || ||| | | | | | | | | || ||| | | || ||| | | | | | || ||||||| ||||| || || ||||| |||||| ||| || ||||||||||| ||||| ||| |||| ||||||||| |||| || || |||| | ||||
------------------------------ctgtacccactgcccagatgggttttggt-tttgtcagtacccatccaacaagtgatgta-----gttcttttttaggtgatttatggccttttgctatttttcagACTCTTGCTGCAACTAATATGGATAATCAAGGACTCACTGAGACCATGCAGAAGCTACTTCTTGTTATGCAAAGATTAGACGAAAAAATTGCACCAATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagatttgtgacggaaattgcttataaagatatccgtttctcttttccttctagACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
tatccgtttctctttt CT-rich tract
aaattgcttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttatctccttacaagctctagagtctatcttctctccctgtgtggaacacaatgtgtatgaacagataaatagatagagatttgtgacggaaattgcttataaagatatccgtttctcttttccttctagACTCTCGCTGCTACCAACTTGGATGATCAAGAACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG