Sequence
atgc intronic sequence ATGC exonic sequence...aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
Basic information
species | Glycine max |
transcript | GLYMA03G40880.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
----------------------------aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagctt--ttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCC-TGCAAGTACAGTCCTG--
| | | || | | || || | |||| | || || || | || |||||||||||||||||||| ||||||||||| |||| || ||||| |||| ||||| | | | | | | || || | || | | |
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 3'ss of exon 4
----------------------------aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagctt--ttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
| | | || | | || || | |||| | || || || | || |||||||||||||||||||| ||||||||||| |||| || ||||| |||| ||||| | | | | | | || || | | |||
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTG
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 4
-----------------------------aaaaattggttagcta--gattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
| |||| || | | | | | || || | ||| | | || || | ||| | ||||| | |||||||||||||||||||| || |||||||| || || ||||||||||| | |||||| ||| | || |||| | |||
gaacaaggtcttaatacatatgtattgttacaaatacgtaaccaaacaaagcctaccggatattatcatgtattaagattctttat-gctgtggacttcagAGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTG
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
-------------------aaaaattggttagctagattttttgtttatgttttaatgagatcac-----------tttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
| || || || ||| ||| | | || |||| ||||| | || || || |||||||| |||||||| || ||||||||||| ||||| || ||||| |||| ||||| | || | | ||| | | || || | | ||
ttgcaagttctaattaacttatgcttcatttttcttatctttggttcgttgaacatcgatatcatgcatttatctgtttgtcataaatgcttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 3'ss of exon 4
--------------------aaaaattggttagcta-gattttttgtttatgttttaat---------gagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
||| | |||| | | | | | | | | ||||| || || || | | || || || ||||||||||||||||| || ||||| | ||||||||||| || ||||||||||| | |||||| |||||| | ||||||||
aaggattatatgcttgatacctttcttgtatggctacaactctctctctctctcttaattataaatatgacatgctgttttcatttatttaaatatgcagGGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGCATACTTG------
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ35213 (Selaginella moellendorffii), 3'ss of exon 4
--------------aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGC----CTGCAAGTACAGTCCTG
|| | ||| | |||| | ||| | | | | ||| ||| | || || | | |||||||||||||| ||||| || ||||| |||||||| || |||||||| || ||||||| || | || || | | | | | | ||| |
gttggtctcaacccaagctctttttatcaagatcat--gttcttactagagttctttcatttttctcaa----ctttctcacagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTTCTCCGGCAAAGCGATTGTTGAGAAGCTACAAAGCGATGATTCCCGTCTT-
upper sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24149 (Selaginella moellendorffii), 3'ss of exon 4
--------------aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGC----CTGCAAGTACAGTCCTG
|| | ||| | |||| | ||| | | | | || ||| | || || | |||||||||||||| ||||| || ||||| |||||||| || |||||||| || ||||||| || | || || | | | | | | ||| |
gttggtctcaacccaagctctttttatcaagatcat--gttcttactagagttcttccatttttctcaa----ctttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTTCTCCGGCAAAGCGATTGTTGAGAAGCTACAAAGCGATGATTCCCGTCTT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
tattgat putative branch site (score: 3)
ttaaaagcttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagcttg