Sequence
atgc intronic sequence ATGC exonic sequencegtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaagcttatattgctttctctttatgccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAGTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
Basic information
species | Glycine max |
transcript | GLYMA04G06080.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 9
gtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaagcttatattgctttctctttatgccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTC--AGTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
| | |||| || | ||| |||| | | | | | || | | | || | || ||||| | | || | || ||| | | ||| || || ||| ||||| |||| || || ||||| ||||||||||||||||||||| | |||||||||||| |||||| || || || | | ||||| |||
----------------------------------------------------------------------------------tttttttataatacttctca------ctggtgtg-actaaacaagttaagatggatttcctt--gtatgttagtggaactaaaatgatgttgggatttttttttgtt--agATATCTTGCATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCAC--
upper sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaa--gcttatattgctttctctttatg----ccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCA--GTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
|| | ||| ||| || ||| ||| | | |||| || || | |||| ||| || ||| || | |||| | | ||||| |||||||| || ||||| ||||| ||||| ||||||||||| |||| ||||||||||||| || | || || ||||| ||||||||||
---------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttgttt-ctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattatggtttgttaattatcccaagcttatattgctttctctttatgccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAGTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
tgttaat putative branch site (score: 3)
tattgctttctcttt putative PPT
tttgttaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaagcttatattgctttctctttatgccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAGTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG