Sequence
atgc intronic sequence ATGC exonic sequencegtaaatattggattaaatcaaattactaagcatggcttctttactatgaataagctaactattttatttttttgcattatcatgactctaatattaaaatttcaactgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
Basic information
species | Glycine max |
transcript | GLYMA06G16680.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 3
gtaaatattggattaaatc------aaattactaagcatggct-tctttactatgaataagctaactattttatttttttgcattatcatgactctaatattaaaatt-tcaactgtatatgattttgg--attacgttgt--cagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
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gtaaataatggttttgtgctccccagtcttttctatcatgcccattataaatattatcctaccagatatgtatccaggttactgtactataacctttcttttaatgttgtaagttgtatcaagtgctaattgtttggttctaacagGGAAGAGTTAGAAATCTTTTCAAAAGAAGTTGTTCGATTTGGAAATCGTTGCAAGAATCCTCAATGGCACAGCTTGGACCGCTACTTTGAAAA
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 3
----gtaaatattggattaaatcaaattactaagcatggcttctttactatgaataagctaactattttattt-ttttgcattatcatgactctaatattaaaat----ttcaactg-----tatatgattttggat------------tacgttgt----cagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
|| |||| | | | || ||| || || | | | |||| | | |||||||||| | | |||| | | || | || |||| ||||||| |||||| || | | | || | || |||| | |||||||| || || ||| || || |||| ||||||||||||| ||| ||||||||||||||||| | ||||| |||||||| ||
gttagtgaataatct-ctgattctttttataaactataacaattgtc---tgaaccatttgtttattttatttatctagcatcaacctggttatatagaagaaatgtacttcaacttgtttttatatgcttgtagttacctgaagtttttatttggtccaacagGGAAGAGTTGAAAGTGTTCTCTACAGAAGTTGTTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCACAACTTGGACCGCTACTTTGATAA
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaaatattggattaaatcaaattactaagcatggcttctttactatga-ataagctaactattttatttttttgcattatcatgactctaatattaaaatttcaactgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
|||| ||| || ||| | || | | | | || | | | || || || ||| | | | | | | | | | ||||| ||| || || | | || | | | ||||| | |||| | || ||| | | ||||| ||||| ||||||||||||| ||| ||||||||||||| ||| | ||| | |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattat-ggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaa-----acaataccttaatt-agttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 2
------gtaaatattggattaa-atcaaattacta-agcatggcttctttactatgaataagctaactattttatttttt-tgcat---------tatcatgactctaatattaaaatttcaa-ctgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
| | || || |||| | | || || | || | | | || || |||| | || || ||| || || | || || | ||| || | || | | || | | | ||||| | ||||| | || || | | ||||| ||||| |||||||| |||| ||| ||||||||||||| ||| | ||||| |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttatccatgcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtattgtgccttttatttttatattgaaaacaataccttaatt-agttaattccatcagGGAAGAGTTAGAAGTATTCACAAAAGAGGTCATTCGCTTTGGAAACCGTTGCAAGGATCCTCAGTGGCATAACTTGGACCGCTACTTTGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgactctaatattaaaatttcaactgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
ctctaat putative branch site (score: 3)
taatattaaaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatattggattaaatcaaattactaagcatggcttctttactatgaataagctaactattttatttttttgcattatcatgactctaatattaaaatttcaactgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA