Sequence
atgc intronic sequence ATGC exonic sequencegtttgttatcgttaacctttttttattttattttattttttttcttgttcaatttctaggcttttttattgttcacttttttttttgttcaaattttttgtttttggtttttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
Basic information
species | Glycine max |
transcript | GLYMA13G30860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G30860.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 1
--------------gtttgttatcgttaacctttttttattttattttattttttttcttgttcaatttctaggcttttttattgtt----cacttttttttttgttcaaatttt-ttgtttttggtttttagTTGAGAAT---TACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
| | | | || | | ||| | |||| |||| |||| | | |||| || | | || | ||| ||| | | || || | | || || | ||| || || || ||||| ||||| | ||||||||| | |||||| ||| || |||| ||||| |||||||||||||||| ||||||||||||||
gttcgtggatgatggcctatgggggactggggattctggaaatttttagggctatttcgtgtttgatttgtcgatttttcgatcgaaacagccctgtgatttctgtgcttacttggttttgtctgtgttgctgcagAGGATCCGTATCCAAATGAGACGATGAGAGCGGAGTTGTCTGTGAAGTTAGGGCTGACGGACAGGCAGCTGCAGATGTGGTTCTGCCACCGGCGGTTGAA
upper sequence: GLYMA13G30860.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g48170.1 (Oryza sativa), 3'ss of exon 1
gtttgttatcgttaacctttttttattttattttattttttttcttgttcaatttctaggcttttttattgttcacttt---tttttttgttcaaattttttgtttttggtt--tttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
|| || | | |||| ||| ||| || ||| ||| ||||| || | || |||| |||| | | |||| | || | ||| ||| | |||||||||||||| || ||| |||| |||| | |||| | || ||||| || ||||| |||| ||||||||||||||||||||| ||||
gtgcgtggattctgatggttttgcgaggc-tttggaagtttggagaattttttttggaggatttttgggtggggaattgaggttttggtgtttggggatgtgattttggtttggtgcagTGGAGCAGTACCCGTCGGAGACCTTGCGGGCGGAGCTGTCCGCGAAGATAGGCTTGTCAGACAGGCAGCTGCAAATGTGGTTCTGTCACCGGCGGCTGAA
upper sequence: GLYMA13G30860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 1
gtttgttatcgttaacctttttttattttattttattttttttcttgttcaatttctaggcttttttattgttcacttttttttttgttcaaattttttgtttttggtttttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
|||| | | | | | | || | || || | | |||| | || | ||||| | | ||| | ||||| |||| | ||| ||| | ||||||||||| ||||| || ||||| |||||| |||| | ||| ||||||| ||||| |||| ||||||||||| ||||| || | ||
------gttcgtggatttcgatgaagtgttttgtgttcttccccaccctggatttttggg-tgctttatcgattgagcatttccggg----ggtttttggtttgctgc----agTGGAGCAGTACCCGTCGGAAGCTATGCGGCTGGAGCTGTCGGCGAAGATAGGGCTGTCGGACAGGCAGCTGCAAATGTGGTTCTGCCACCGCCGCCTCAA
upper sequence: GLYMA13G30860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 1
---------------------gtttgttatcgtta--acctttttttattttattttattttttttcttgt----tcaatttcta---------ggcttttttattgttcacttttttttttgtt-----------caaattt---tttgtttttggttt--------------ttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
| |||||| ||| | || |||||| || ||| |||||||| || | ||| || | || ||| | | || | ||| |||||| | ||||||| |||| |||||||| | ||| || || ||| ||||| | | | | ||| |||||||||| || |||||||| || |||| || ||||||||||| ||||||||| |||||||
gtatgtattctggttttccttttctgttattattattattttattttatgttttttggtttttttttttatgtgatcagctttgattttggtttgggtttggtgtggtgaagtttggtttttggtttgatgtgatgcaaatttggttttggctttggtttgatgtgatttttgatcagTGGAACCGTATCCGACGGAGGCGTCGCGAGCAGAGCTGTCGGAGAAATTAGGGTTGTCAGACAGGCAATTACAGATGTGGTTTTGTCACCGGAGGTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttttattgttcacttttttttttgttcaaattttttgtttttggtttttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
ttttttgttttt CT-rich tract
ttttttttttgttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttatcgttaacctttttttattttattttattttttttcttgttcaatttctaggcttttttattgttcacttttttttttgttcaaattttttgtttttggtttttagTTGAGAATTACCCGTCGGAGACTATGAGGGTGGAGTTGTCGGAGAAGTTGGGGTTGTCGGATCGGCAGTTGCAGATGTGGTTCTGTCACCGGCGGTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG