Sequence
atgc intronic sequence ATGC exonic sequencegtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
Basic information
species | Glycine max |
transcript | GLYMA13G27210.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 16
gtgattttcaatctattt--ccacattttctaactttcttgtataa----atgcttaatctatttattttttcct--agAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
||| | | | | | | | | | |||| ||| | | || | ||| | ||| |||| || ||||||||||||| |||||||||| ||||| |||||| | |||||||||||||| ||||| | || || || ||| | ||||| || ||
gtgggtcttaccttttctagtgataacctaggacttactttaaaagcagcatacgtaaaccttttgttttcatctgcagAATGACAAGTCAAAAATCAAGACAGTGATAGAAGAGTTGGATGAGAAGAAGAAAGAGACCTTGAAAGTCACATGGCTTAAAGTAAACAA
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G006452_T02 (Zea mays), 3'ss of exon 10
---------gtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcc-tagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
| || | || | | | | | | | || | || ||| || | || | | || ||||||||||| | ||||||||||| ||||| || ||| | ||||||||||||||||| ||| | || || || ||| ||||||| || ||
gtatctcctatcatgtacagttt-tcttgataaactgaaagtagttttaatatctgggcacataccttgtctcatctgcagAATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAA
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
--------------------gtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
| ||| |||| |||||| | | ||| | || | || || | ||||||||||||||||||| || ||||||| ||| ||||| || ||||| ||||||||||| || || || || || ||||| ||| | ||||| || |
gttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggt---ttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
-------------gtgattttcaatcta-tttccacattttctaactttcttgtataa-atgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
| | | ||| || ||| | | || ||| || | ||| || | | ||| ||||| |||| |||||| || ||||||||||| || ||||| ||||| ||||||||||| || || ||||| || ||||| ||| | ||||| || |
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 16
----gtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
|| | ||||||| || || || || ||| | | | | |||| || | ||| |||||||||||||| |||||||||| ||||||||||||||| ||||| ||||||||||| ||| | || ||||| |||| ||||| || ||
gtttgtagctctcaatctgttgacatgttgtcatactatgattt-----tacttatgataatatgcctttaatagAATGACAAGTCAAAAATCAAGATGGTGATTGAAGAGCTGGATGAAAAGAAGAAGGAAACATTAAAGGTTACTTGGACTAAAGTTAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
tctatttattttttcc CT-rich tract
tttcttgtataaatgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA