Sequence
atgc intronic sequence ATGC exonic sequence...ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
Basic information
species | Glycine max |
transcript | GLYMA13G21230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 3'ss of exon 4
--ttacgcagacctttgatta----tctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
| | || |||| || || ||| | | | | || | | | | | | | | | || | ||||||||||||| ||||||||||| | |||| | ||||| || || || ||||| || || |||||||| || |||||||| | |||| | | ||| |||
ggtgctaggaatctatgatcggactactgctatattccaatcttacccttataatgcttctgcggttctgccctataattttttttggtcatg------gctgcagGATATGTTTGAGGAGAAAAGAAGCATACTTGAACCTGCTGGTGCCCTTGCGCTGGCAGGAGCTGAAGCTTACTGCAAATACTATGGCTTGAAAGGGGAAA
upper sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
| || | || || || || | || || || | || | | | | | || | ||| || | | ||||||||||| ||||||||| |||||||||| ||||||||||| || |||||||| |||||||||||||||||||| || || |||| | ||| |
--gtatggtactatccttgatacgt-tatcccttgtcagacggtg----tttggcatatgcatactgaattgtagataatcaga-tacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
upper sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
--ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaact--tgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
| | |||| | | || | ||||| | || || | | | | ||||| | | | | ||| |||||||| | ||||| ||||||||||||| ||| |||||||| ||||| || ||||| || ||||||||||| || |||||||| || | || ||| |||| ||
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacat---ttgggtgttgttgaggtctttggagt-tagaatttttggtactgatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
acttaat putative branch site (score: 4)
tatgacttaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - gcagacc
- - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa