Sequence
atgc intronic sequence ATGC exonic sequencegtctgtgatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcattttagatgatttagtgtagagagaataacatttttttttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT
Basic information
species | Glycine max |
transcript | GLYMA12G03260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 3
gtctgt---gatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcatttta-gatgatt-tagtgtagagagaataacattt--ttttttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT------
|||||| ||| | || || | || | |||| | || ||| | | | || | | || ||||| | ||| | | | || || | |||||| |||||| |||||||| |||||||||| ||||||||||||||| ||||||| ||||| |||| | |||| ||||| || ||||| ||
gtctgttttgattggtaagaggcttccctgtcacttaatttcttttgctgactactatagtagtatggtcatcaccgtgtattcaaaatcctgtctgatattgcttcctctcccagTTGTGGCAATGTAAACTTTGCCTTTCGTGGTGTCTGTAATCGCTGTGGAGCTGCTCGCCCTGCCGGTGTTAGTGGA---TCAGGTGCCGGTGGTGGTGGTAGG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 3
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcattttagatgatttagtgtagagagaataacatttttttttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT---
|| | || | | ||| || | | || || | |||| |||| | | ||| | | || | | ||| ||| ||||| || |||| |||||| || ||||| || ||||||| |||||||||||||||| |||| || |||||||||||| ||||| | | | | ||||||| ||
gtgagcgacttctctatcactt-cagttcactagttgactagtattgtattca--cattgttattcttttttttttgattatctgagattatttattctccca-----gTTGTGGCAATGTAAATTTTGCCTTCCGTGGTGTTTGTAATCGCTGTGGAGCTGCACGCCCTGCTGGTGCTGGTGGAACTGCTGCTGGTGGTGGCGGTAGG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: AC185415.3_FGT005 (Zea mays), 3'ss of exon 3
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcact--tcagtcattttagatgatttagtgtagagagaataacatttttttt-------tctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT---
|||||| || |||||||||| || | ||| | |||| ||||| | | | | | |||| | | | || | | | ||| | |||||| |||||| || ||||| || ||||||| |||||||||||||||| |||| || ||||| |||||| ||||| | || | |||||| ||
gtctgttatg----attggtgagcgact-tctctatcacttcagttcactagttgactagtatggtcttcacagtgctatcattctttctgattatctgagatgatttcttctctcagTTGTGGCAATGTAAATTTTGCCTTCCGTGGTGTTTGTAATCGCTGTGGAGCTGCACGCCCTGCCGGTGCTGGTGGAACTGGTGGTGGAGGTGGCGGTAGG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcact--tcagtca--ttttagatgatttagtgtagagag-aataacattttttt-ttctctcat-agCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT---
||||||||| ||| || |||||| |||| ||| |||||| | | | | | | ||||| || |||| || || | || || | | ||| |||| ||||||| | |||||||| ||||| || ||||| | |||||| ||||||||||||||| | || |||||||| ||||| || || ||| |||
gtctgtgatgtgatatcggtgaggagcttcatctagctcttgtttccgttaatttgctagtttttatatattttatagtttctagcagtagtgttctcatactctttcattggcagTTGTACAAATGTGAATTTTGCATTCCGTGGGGTTTGTAACCGCTGTGGAACTGCTAGACCAGCTGGTGCATCTGGTGGCAGCATGGGTGCTGGTCGTGGA
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 2
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcattttagatgattt--------agtgtagagagaataacattttttt---ttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTT---CAGGGGCTGGTGGCCGT
||||||||| ||| ||||||||||||||||||||| |||| || | ||| | | | | ||| | ||| | | | || || | | | | ||||||||| || || ||||||||||| |||||||||| || ||||| ||||||| |||||| ||| |||||| ||||| | | ||||||| ||||| ||
gtctgtgatgtgagattggtgagcagctctttctttttcttttatactcttttcttgtgtagtgtattttcaaaaaccattgttatgcatttggctttcttatatgctatgtggtagcagTTGTTCGAACGTGAACTTTGCATTTCGTGGTGTGTGCAATCGTTGTGGAAGTGCTCGACCTTCTGGTGTGTCTGGCAGTGGTGCAGGGGCAGGTGGTCGG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 2
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcattttagatgattt--------agtgtagagagaataacattttttt---ttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTT---CAGGGGCTGGTGGCCGT
||||||||| ||| ||||||||||||||||||||| |||| || | ||| | | | | ||| | ||| | | | || || | | | | ||||||||| || || ||||||||||| |||||||||| || ||||| ||||||| |||||| ||| |||||| ||||| | | ||||||| ||||| ||
gtctgtgatgtgagattggtgagcagctctttctttttcttttatactcttttcttgtgtagtgtattttcaaaaaccattgttatgcatttggctttcttatatgctatgtggtagcagTTGTTCGAACGTGAACTTTGCATTTCGTGGTGTGTGCAATCGTTGTGGAAGTGCTCGACCTTCTGGTGTGTCTGGCAGTGGTGCAGGGGCAGGTGGTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtcattttagatgatttagtgtagagagaataacatttttttttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT
gaataac putative branch site (score: 2)
catttttttttctctc CT-rich tract
agaataacattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtgatatgaaattggtgagcagctctttcttgctcttctactcacttcagtcattttagatgatttagtgtagagagaataacatttttttttctctcatagCAGTTGCTCCAATGTGAACTTTGCTTTTCGTGGTGCTTGTAATCGCTGTGGAACTGCTCGTCCTGCTGGTGCTTCTGGAATTTCAGGGGCTGGTGGCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG