Sequence
atgc intronic sequence ATGC exonic sequence...aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
Basic information
species | Glycine max |
transcript | GLYMA08G08720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g47560.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatg---gc-caaagtgaaaaatgaagttt--aataga-tgatgaatatgatgataatt-----gcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| || | | | | ||| | | | || | | || || | || ||| |||| ||| | | | ||| |||||||||||||||||||||| || ||||||||| | |||||||| || |||||| |||| | |||||||| | ||||| || ||||| || || |
gtacgtatgtacagttacacacacgtatagtacgtgactcgtagctgtgcgcgtgtacgtgtaccggccgcagtagttgcaccggacgcgcgcgcgcgcggcagaatgcgatgattgcaatgatctgatatatacggggttgatttttttgcagGAGCTACTACAGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACCCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g49100.1 (Oryza sativa), 3'ss of exon 2
--aatggtttcgatttgtttaatttaattaccaatat-tgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| | || | || | | | |||| || | | | || | | | | |||| ||||| || ||| ||||||||||||||| ||||||| || ||||||||| | |||||||| | |||||| |||| | |||||| | | ||||| || || || || || |
ttatgaatcatgaatgcatttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgt---gtgatggatggatggatgggtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151763_T01 (Zea mays), 3'ss of exon 2
--aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| || || || | | || || || || | | || || | | | | |||| | || | || ||||||||||||||| ||||||| || ||||||||| | |||||||| || |||||| |||| | |||||||| | ||||| || ||||| || || |
cgcacagtgtccatgatgtagctatagctagacatgctgcgtttgcgtgagctaatggtgggagcgctgcgaccgtgatggcgcgtacgt--gtacgtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCCGTGAAGAAGCGGGTGGAGCGGTCGTCCCAGGACCCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G453571_T01 (Zea mays), 3'ss of exon 2
aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatg-ataattgc--agGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| |||| | | | | | | || | || | || ||| | | | |||| | |||||||| || || |||||||||||| ||||||| || ||||||||| | |||||||| || |||||| |||| | |||||| | | ||||| || ||||| || || |
tagggttcccacacg---acacgagcgagcagcaatgagcatatggtgaccacgtcgtactgactgatacaataatgcaacgatatgatgcatgggcgcgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G812272_T02 (Zea mays), 3'ss of exon 2
----------------------------------------aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataat-tgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| ||| | | || || | | | || | | | | | | | | || | |||| | ||| |||| ||||||||||||||| ||||||| || |||| |||| | |||||||| || |||||| |||| |||||||| | ||||| || ||||| ||||| |
gtacgtggtacatgcacagcacgtatatacagctatacctactggctactgcacgtatatacagcacctctcttcgatcctactccatgacgtacggtacggtagacattgctgcatgagcta-atggtgatggcgtgcagGAGCTACTACCGGTGCACGACGCAGAGGTGCCCCGTGAAGAAGCGGGTGGAGCGGTCGCACCAGGACCCGGCGGTGGTGATCACCACGTACGAAGGCAAG
upper sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
lower sequence: AC198725.4_FGT009 (Zea mays), 3'ss of exon 2
------aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
| || ||| | || | || | || | || | | || | | | | || | || | || | | || ||||||||||||||| |||||||||| | |||||| |||||||| ||||||||| |||| | |||||||| | || ||||| || ||||| || || ||
atctctcaccaagagtatgtgtatgatgcatgtatgtaccttacaataac--ttgtcata-catatattcaaatccgatctccggccaa-acgc--atgcatgcagGAGCTACTACCGGTGCACTACGCCCAAGTGCGGCGTGAAGAAGCGCGTGGAGCGGTCGTACCAGGACCCGTCGACGGTGATCACGACGTACGAGGGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
gtttaat putative branch site (score: 4)
aaaaatgaagtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtttcgatttgtttaatttaattaccaatattgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg