Sequence
atgc intronic sequence ATGC exonic sequence...tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G32510.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
|||||||| |||| || ||||||||||||||| |||| || |||||| ||||||| |||||||| |||||||| || | ||||| || || ||
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC--------------------------------------------
upper sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
|||||||| |||| || ||||||||||||||| |||| || |||||| ||||||| |||||||| |||||||| || | ||||| || || ||
gtacaagctgttctatatcctttttgttgtgtttatggacttctaataacctgagttcagtctgtctgtgaagtttgttcattacaagttccttttttggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC--------------------------------------------
upper sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| || || || |||||||||||||| ||
gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC--------------------------------------------
upper sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||| |||||||| || ||||| ||
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC-------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
tcccatc CT-rich tract
aactgtttttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
- - - - -tcaaccc
- - - - - - - - - - tgcttta
- - - - - - - - - - - - - -caacagc
- - - - - - - - - - - - - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgga