Sequence
atgc intronic sequence ATGC exonic sequence...attcagattatctttatccctgttgcctcataccatcatattggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
Basic information
species | Glycine max |
transcript | GLYMA04G08550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G08550.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 3
attcagattatc-tttatccctgttgcctcataccatcata--ttggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
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aggcatcatatggtatgtctttgcaaattcattcaattatgggtactataaatgtgttaactgtagtttctctaaccatggattagcttatctgatt---cagGTGGCACAATCATCTTAACCCAGCCATAAACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGG
upper sequence: GLYMA04G08550.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
--------attcagattatctttatccctgttgcctcataccatca-tattggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
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gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgat--atagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
upper sequence: GLYMA04G08550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 5
attcagattatctt----tatccctgttgcctcataccatcatattggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
| |||||| | | | || ||| || | |||| ||| | || | || || || || || || | | |||||||| |||||||| |||||| | ||||| |||||||||||||| ||||||||||| ||||| | || | || ||||| ||||||||||||| |||
tctatgattattctatgatgtttcttttggcttttg--atcactttgttaggatgagaatgtgctactt--tttctacttgcatggattgatccttcctttcagGTGGCACAATCATCTAAATCCTGCCATAAACAAGGAAGCATGGACTCAAGAAGAGGAACTGGCTTTAATTCATGCTCATCAAATTTATGGGAACAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
agttaat putative branch site (score: 4)
ttaattctcgtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcagattatctttatccctgttgcctcataccatcatattggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - -atccctg
- - - - - - - - - - - -tgcctca
- - - - - - - - - - - - - - - - ccatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggatgt