Sequence
atgc intronic sequence ATGC exonic sequence...agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
------agagaaaaaaaaatgct--gtgagcattacttaa-atctgcagtttgttac--cttatagtctttccaatgcttattatgtcaattttcattgtgaatttg---gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
| | | | || || | | || || |||||| | | | ||| || | | || || | ||| | | || || |||| ||||| |||||||||||||| |||||||| || |||||||||||||| ||||||||||| || || | || |||||||||||| | ||| ||||||| ||||
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
------agagaaaaaaaaatgctgtgagcattactta-aatctgcagtttgttac----cttatagtctt----tccaatgcttattatgtcaattttcattgtgaatttggt-agGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
| | | | || || ||| ||| || | | | ||| | | ||| || | || | | || || | | | |||| |||| | |||| |||||||||||||| |||||||| || |||||||||||||| ||||||||||| || || | || |||||||||||| | ||| | ||||| ||||
gtatacaagtaggagcacatact-tgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttatta-----tgtcaattttcattgtgaatttg---gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
| | || | | | | | | ||| |||| | | || ||| | |||| || || | | ||| || |||| ||||| |||||||||||||| |||||||| || ||||| |||||||| ||||||| ||| || || | || |||||||||||| | ||| | ||||| ||||
-gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
------------------agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgt-taccttatagtctttccaat---gcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
||| | |||| | | || ||| || | | | ||| | | |||||| | || ||||| | | || || | || |||||||||||| ||||||| ||||| || || ||||| || ||||| ||||||||||| |||| || |||||||||||||| | || | ||||| || |
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
--agagaaaaaa-aaatgctg-----tgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
|| ||| || | || || ||| | || | | | || | | | | ||| |||| | || ||| | ||| ||||| ||| |||||||||||| ||||||| || || || || ||||| || ||||| ||||||||||| | || || |||||||||||||| | || | ||||| || |
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcct-ttttgtaatattt--ttgtgc-tttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
--------------------------------------------agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgttaccttatagtctttccaatgc-ttattatgtcaattttc-------attg---tgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
| | | | || | | || ||| | || || ||| || | | | | |||| | ||| | |||| |||| ||||||| |||||| ||||| ||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||| || |||||||||||| | || || || || ||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
agagaaaaaaaaatgctgtgagcattacttaaatctgcagtt-tgttaccttatagtctttccaatgcttattatgtca-attttcattgtgaatttg-gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
|| | || || || | | | | | |||| | | || || | | | ||||| | | || |||| ||||||| | ||||||| || |||||||||||||||||||||||||| ||||||||| |||| ||||||| || || |||||||| ||||| | || || || || || |
--ggagtattggattctctg-gtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
ttattatgtcaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - aaaaaaa
- - - - - - - gctgtga
- - - - - - - - - - -gcattac
- - - - - - - - - - - - - - - - -tctgcag
- - - - - - - - - - - - - - - - - - - - - tgttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgctt