Sequence
atgc intronic sequence ATGC exonic sequence...gtgtttttcatacaccattcatgctagtgtggctgaggttatcttgatcgtcacttaatatactctttatagttatttctaattgttatattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
Basic information
species | Glycine max |
transcript | GLYMA03G02610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtttttcatacaccattcatgctagtgtggctgaggtt---atcttgatcgtcacttaatatactctttatagtt-atttctaattgttatattcct-cctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
|| | | || || || ||||| || | | ||| | | | || | | | || | || || || | | | ||| || | ||||||||||||||| || |||||||| |||||||| || ||||||||| | | || ||| | ||||||| || || ||| | | |||||||| ||||||
--gtatgttatgt-cccttgatgcttcgctgtttaaagtttaagtttcgttca--ggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------gtgtttttcatacacca--ttcatgctagtgtggctgaggttat---cttgatcg--tcacttaatatactctttatagttatttctaattgtt--atattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
| | || | || || || |||| | | || || | || | || | || || || | | | || | | || | ||||||||||||||| || ||||| ||||||||||| || ||||||||| | || || | ||||||||||| |||||| | | || ||||| ||||||
gtatgatctaatatcttgttgtggcttatctttacgccctgaatctatttattttgtggtatcagagctgcgatcattaactagtgcgaactatttgaagtagcattcatttctgtattggttttcttgaccttgtttttagGATGGTCAATGGTCTCCTTAAGACTGCTCAAGGAGTGCCTCCTGGTACAGTTACTACCTTGTTGCCACCTCAGGAAGCAGCCATGAAGCTTGAAGCCATG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 2
gtgtttttcatacaccattcatgct-agtgtggctgaggttatcttgatcgtcacttaatatactctttatagttatttctaattgttat-attcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
|| ||| | | | | | | | ||| ||| |||| || || | | || |||| || || ||| | |||| || || | || ||||||||||||||||||||||||||||||||||||||||| || || | || ||||| || ||||||||||||| || | |||||||| || |||
gtttttcttctgtcctaatggttttgagtatggttgag-ttggctaaggtttaaatttttatatgggttggtgtc-cttcacttcattattgttacttccagAATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCAGGCGTTGCCACTACACTGTTACCACCTCAAGAAGTGACCATGAAACTTGAAGCTATG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15473 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttttcatacaccattcatgctagtgtggctgaggttatcttgatcgtcacttaatatactctttatagttatttctaattgttatattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
| || || | || | | | || || || | | ||||| |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
-----------------------------------------------gtatgcctcgattgaa--ttcaagttcttcgctgataatttgctattttctagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttttcatacaccattcatgctagtgtggctgaggttatcttgatcgtcacttaatatactctttatagttatttctaattgttatattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
| || || | || || | | || || || | | ||||| |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
-----------------------------------------------gtatgcctcgattgaa--ttcatgttcttcgctgataatttgctattttctagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcgtcacttaatatactctttatagttatttctaattgttatattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
ttctaat putative branch site (score: 2)
tattcctcct putative PPT
ttaatatactctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttttcatacaccattcatgctagtgtggctgaggttatcttgatcgtcacttaatatactctttatagttatttctaattgttatattcctcctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - catacac
- - - - - - - - - tcatgct
- - - - - - - - - - - - - - -tggctga