Sequence
atgc intronic sequence ATGC exonic sequencegttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
Basic information
species | Glycine max |
transcript | GLYMA09G04280.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
-----gttcgtttcttcaatttctgtg-----acaaaaaattcttctaattttgtgcttttt-ttctgttcttctcttcccatcgtcttttaatttttgtgccactt------gatt--gcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
|| ||| || ||||| | | | | | | |||| | | || || | ||| || | || | |||| ||| | | | | |||| | |||||||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| ||||| |||||||| |||||| | || ||||| |
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
-----------gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| | || | | | || | | | | | | || | | | | || | | | | ||| | | |||| | | ||||||||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| |||||||||||||| |||||| | || || ||
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCG--GAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
------gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtct--tttaatttttgt--gccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| | | | | | | | || | | ||| || | || | | || | | | ||| || ||||| || | ||| ||||| ||||||||||| ||||| || ||||| ||||| | |||||| ||||| |||||||| |||||||||||| | || |||||
gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| || | | || | | | | || | | | | | ||| | || | ||| ||||| ||||||||||| ||||| || ||||| ||||| | |||||| ||||| |||||||| |||||||||||| | || |||||
---------------------------gtgtgattttcgtctt-caccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| | || | | | | | || | | || | | | | || | | | | | ||| | || | ||| ||||| ||||||||||| ||||| || ||||| ||||| | |||||| ||||| |||||||| |||||||||||| | || |||||
gcaccccgctcgatctcatcctaatcggtgtgattttcgtctt-caccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttt--tttctgttcttctcttcccatcgt-cttttaatttttgtgccacttgattgcag-
| ||| || | | || || ||| || | || | | |||||| || | | || | ||||| | || ||| |||| ||||||| ||||| ||||||||||| |||||||| |||||||||||| |||||| || || |||||||| |||| || | | ||
--ttagttcggagatgatttagttgaat--tttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
gttcgtttct--tcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-
||||| | | | || | | ||||| | | || || || || |||| | || | ||||| | || ||| |||| ||||||| ||||| ||||||||||| |||||||| |||||||||||| |||||| || || |||||||| |||| || | | || |
gttcggagatgatttagttgaattttggaggattct--gggtagttagcattggagcttctccatgtttcctg----cattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgt-gctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-
| ||| | | | | | | | ||| | | || ||||| | |||| || | | | |||||| || || | |||| ||||||| ||||| ||||| ||||| || ||||| |||||||||||| |||||| || || |||||||| |||| |||| ||| || |
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtctt--gattgac---tgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
gttcgtttcttcaatttct---gtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-
| | | ||||| ||| || | | || | || || | ||| | | | | | |||||| || || | |||| ||||||| ||||| ||||| ||||| || ||||| |||||||||||| |||||| || || |||||||| |||| |||| ||| ||
---tgcagcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
tcttttaatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG