Sequence
atgc intronic sequence ATGC exonic sequencegtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
Basic information
species | Glycine max |
transcript | GLYMA19G43320.4 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 10
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
||| || | | | ||| || || | || | |||| | ||| |||||| | | || ||| | || | | | | | | ||| |||||| || |||||| |||||||||| || || ||||||||||||| |||||| || ||||| ||||| || ||||||||||||
----------------------------------gtaaaatatgttcttagccaactggttta---tgcatactgccttgtcgtaaagtgcat----agtttatctaatttatctggatttagtgat-acaactctgtggactttcc-----agGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g01930.t01 (Vitis vinifera), 3'ss of exon 11
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcat-------agGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
|||||| || | | || | ||| || | |||| | | ||||| | || | || | | | || || || |||| ||||| | ||||| | | | || ||| || ||| | |||||| |||| || || |||||||||||||||||||||||||| ||||| |||||||| ||||||||||||
------------------gtactt---ctctgtcacagatatggatat-atttcttgaattatctct-------tcattgtttt--tcttaatcttggacaaatcttttagctctgaactttctcagtattaaatgtttaacctcatactttttcttaaagCTGGAACAAGAAATTGAATTATATAATTGCTATCGCAAAAGATGGAGTTTATGATGTCACTAAACGCTACACAAGAAAGTGGCATGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: EFJ38670 (Selaginella moellendorffii), 3'ss of exon 7
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
| || | | || || | | | | ||| | || || ||||| || || || || || || || || | || |||||||||||||||||||| || |||||||||||| |||||||| |||
------------------------------------------------------------------------------------------------------gtactatgtgacagttctttttc-tcacgctaacaccggacttgcgtca-agATGGGGAAAGAAGCTGAACTACGTCATT-CCGTTGCGAAAGATGGAGTTTATGATGTTACAAAACGATACACACGGAAGTGGGCAGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: EFJ38668 (Selaginella moellendorffii), 3'ss of exon 6
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
| | |||| | || || || | | ||| | || || ||||| || || || || || || || ||| | || |||||||||||||||||||| || |||||||||||| ||||||||| |||
--------------------------------------------------------------------------------------------------------------gtactatgtgac--agttctttttctcacgcacttgcgtca-agATGGGGAAAGAAGCTGAACTACGTCATTGCCGTTGCGAAAGATGGAGTTTATGATGTTACAAAACGATACACACGGAAGTGGCCAGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: EFJ38667 (Selaginella moellendorffii), 3'ss of exon 6
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
| || | ||| | | | | | | | ||| | || || ||||| || || || || || || || ||| | || |||||||||||||||||||| || |||||||||||| ||||||||| |||
------------------------------------------------------------------------------------------------------gtactatg-tgacatttctttttctcacgctaacaccggacttgcgtca-agATGGGGAAAGAAGCTGAACTACGTCATTGCCGTTGCGAAAGATGGAGTTTATGATGTTACAAAACGATACACACGGAAGTGGCCAGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: EFJ31479 (Selaginella moellendorffii), 3'ss of exon 7
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
| || | ||| | | || | | | | ||| | || || ||||| || || || || || || || ||| | || |||||||||||||||||||| || |||||||||||| ||||||||| |||
------------------------------------------------------------------------------------------------------gtactatg-tgacatttcttttcctcacgctaacaccggacttgcgtca-agATGGGGAAAGAAGCTGAACTACGTCATTGCCGTTGCGAAAGATGGAGTTTATGATGTTACAAAACGATACACACGGAAGTGGCCAGAG
upper sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
lower sequence: EFJ38669 (Selaginella moellendorffii), 3'ss of exon 6
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
| || | | || || | | | | ||| | || || ||||| || || || || || || || || | || |||||||||||| ||||||| || |||||||||||| |||||||| |||
------------------------------------------------------------------------------------------------------gtactatgtgacagttctttttc-tcacgctaacaccggacttgcgtca-agATGGGGAAAGAAGCTGAACTACGTCATT-CCGTTGCGAAAGATGGAGTTCATGATGTTACAAAACGATACACACGGAAGTGGGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
atgtttcctcattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA