Sequence
atgc intronic sequence ATGC exonic sequence...cattgtccagaggctcttcactatgcgaaggtatgggggagggatgttgtacgcagccttacccttgcattttcataatattcaatgttaatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
Basic information
species | Glycine max |
transcript | GLYMA04G00530.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G374574_T01 (Zea mays), 3'ss of exon 4
cattgtccagaggctcttcactatgcgaaggtatgggggagggatgttgtacgcagccttacccttgcattttcataatattcaatgttaatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
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-gtactttgcaagctc------agacaaccatacctctggattatgatatattgaggtatatcat-gtatttcccaacccttcatctatgtgccttacagGTACTAGAGCATGCTTCTGTTTGTTTGACACGCATTGCTGAAGCTTTTGCCTATTACCCCGACAAACTTGATGAACTCTGCAATCATGGATTAGTTGCTC
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 3
cattgtccagaggctcttcactatgcgaaggtatgggggagggatgttgtacgcagccttacccttgcattttcataatattcaatgttaatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
| | || | | || | ||||| || | || | | ||||||| | | || ||| || | || | |||||| ||||| |||| ||| | ||| |||| ||||| ||||||||||||||| | | ||| || |||||||||||||| || || ||||| ||||| || |
------gtaattgacctgctttctgttataatatggtactaatatctagttc-cgctcttaccccagtctcctcc--ataatctgttcgtatgatggtagGTTTTGGAATATGCTTCTATCTGTCTGACTCGAATTGCTGAAGCATTTGCACCGTATCCCGAGAAATTAGATGAATTATGTAACCATGGCCTGGTGACGC
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 3
-------cattgtccagaggctcttcactatgcgaaggtatgggggagggatgttgtacgcagccttacccttgcattttcataatattcaatgttaatttttg-----tagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
| | | | ||| |||| | ||| |||| | || | | | ||| | | || | || | ||| |||| ||||||| ||||| | |||||||| |||||||| ||||| ||||| |||||||||||||| |||||||| || ||||| |||||| | |||||||||||||| || |
gtaagtttgtcattttgtagttct--actacg-gaacttatgatcctgttatagtttttgtt-tcttcctcatgtgtcttttctttcttctttgttgatttttggtttctagGTGTTAGAACATGCTTCTGTTTGCTTGACTCGAATTGCTGAAGCATTTGCTTCATCTCCGGATAAATTGGATGAACTATGCAATCATGGACTAGTTGACC
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 3
cattgtccagaggctcttcacta--tgcgaaggtatgggggagg-gatgttgtacgcagccttaccct-tgcattttcata-atattcaatgt-taatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
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------caagggtctacttcccaaatactgaacagtgccttttgtaatcccttccatagcctttttgtatttattctcgtatataggctgtgtgttatattttcagGTGTTAGAGCATTCTTCTGTCTGCTTGACTCGCATTGTGGAAGCAATTGCTTCATCCCCTGACAAGTTAGATGAACTATGCAATCATGGACTGATCGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtacgcagccttacccttgcattttcataatattcaatgttaatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
tgttaat putative branch site (score: 3)
tttttgt CT-rich tract
attttcataatattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattgtccagaggctcttcactatgcgaaggtatgggggagggatgttgtacgcagccttacccttgcattttcataatattcaatgttaatttttgtagGTCCTGGAACATGCCTCTGTTTGTTTGACACGAATAGCTGAAGCATTTGCATCATCTCCAGACAAATTAGATGAATTGTGCAATCATGGACTGGTAACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - -ctcttca
- - - - - - - - - - ctatgcg
- - - - - - - - - - - - - - - - - - gggaggg
- - - - - - - - - - - - - - - - - - - - - - - -tgtacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt