Sequence
atgc intronic sequence ATGC exonic sequence...tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
-----tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
| ||| || || | | || || | | ||| | || ||||| | | || || | | || | || | | | ||| || ||||||||||| | |||||| |||||||| |||| |||||| |||||||| ||||||||||| | |
tggaatatttgttagttgttggcagctcactactt-aatacttatgtcag-ttatgattg---ccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
tttttcataacat-ttctccttgaattattttgaaatatatctgagattatggatata-tctgtcatttttaaatttttatggttgtgtaatatg------cttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
|| || |||| |||| | |||| | || | | | |||| ||| || | | || || | ||| | || || || || |||||||||||| | |||||| | ||||| ||||| |||||| |||||||| ||||||| || | |
------ggaaaatgttctatactaatt--tctgaacgccacttgtgttgctctttataatctcatatcctgagatgttctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
-tttttcataacatttctccttgaattat-tttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
| | ||| || || | | ||| || | | | | | ||| || | || |||||| || || | ||| ||| || |||||||||||| | |||||| | ||||| ||||| |||||| |||||||| ||||||| ||| | |
atatcctatactggttgagtccgagtgctgcttgtgttactctttataatttc-ataatcctaaggtgttctttgttttatactt-tgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatg------cttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
| | || || ||| || |||| | || | | | |||| |||| | | || || | ||| | || || || || |||||||||||| | |||||| | ||||| ||||| |||||| |||||||| ||||||| || | |
--ctggaaaatgttctatactgattt---ctgaacgccacttgtgttgctctttataatc-tcatcctgagatgttctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------------tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaa----atttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
| | | || | |||| |||| | || | | | | || || ||||| ||| | ||| | | | | |||||||||| |||||||||||||| ||| | ||||| ||||| ||||| ||||| ||| | || ||||||| ||
gtattataatattaaacagtttttttttgttggacatattatagtaaacgcttcttgtatgccttggctaaaccatctccactttggcttcattcttgtgcactttttcaccattaccaatttcttttattgtccttccatttgtaatcccaatttcctaatgtctgttttttcttgcagGCTAGAGAACACATTGAATTATGGCCTTGAGAGAGTCTGGGCAATTGGTTACATTAAAAGTTCACGCCG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------tttttcataacatttctccttgaatta--ttttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
| | ||| | | |||| || ||| ||| | || ||| | | | |||| |||| | ||||| | || || | | | ||||||||||| |||||||||||| | ||||| || ||||||||||||||| || | || |||||||| ||
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatct-tcatccaacagttttt-tactta-atacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
---tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
|||||| ||| | || | | | | | ||||| ||| | |||| | | | | || | | |||||| |||||||| ||||| ||| |||||||||||||||||||| |||||||| |||| |||||||| ||
tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatg--ctagtctttaatttccgacagactgaaccttcttcat-taactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
atttttaaatttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - -ctccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg