Sequence
atgc intronic sequence ATGC exonic sequencegttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
Basic information
species | Glycine max |
transcript | GLYMA11G02030.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
gttatttcatttatgttttccaaatttgaggtttatattcttat-attagct-gttg-ggtcacagttttcctttttattaacaaatgatatat-tcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
| | || |||| | || | || | ||| || |||| |||| | || ||| || |||| || | | | |||| || ||||| |||||||||||| | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattga-aacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
gttatttcatttatgttttccaaatt-tgaggtttatattcttatattagctgttgggtcacagttttcctttttattaacaaa---tgatatatt-caacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
|| | || | | | | | | || | | | ||| | || | | | || ||| | | | | |||||| || | ||| || ||||| |||||||| || | ||||||||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
-ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgctt--cttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
gttatttcatttatgttttccaaatttgaggtttatatt--cttatattagctgttgggtcacagttttcctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
|| | | || | || ||| | | | ||| | | ||| | ||| | | || | | |||| | | |||| || ||||| |||||||| || ||||||||||||| || ||||| || |||||||| || || ||||| ||||| ||||| || ||||| || || ||
gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
---gttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttattaac---aaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
|| |||| | | || | | | || ||| || | | || | || ||| | ||| | || || | |||| || |||| ||| |||| ||||||||||| | ||||||||||| || ||||| ||||||||||||| ||||| || ||||||||||| |||||||| || || ||
gtatttctttctctgaacttgtatacaatta--gttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactct-cagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
gttatttca----tttatgttttccaaatttgaggtttatattctta---tattagctgttgggtcacagttttccttttta--ttaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
|||| | | | | ||| |||| || ||| || | ||| | | | || | || | | |||| ||||| | ||| || | |||| ||| |||| ||||||||||| || ||||||||||| || ||||| ||||| ||||| || || || || | |||||||| ||||| ||||| || ||
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatctt-accagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
gttatttcattt----atgttttccaaatttgaggtttatattcttatattagctgttgggtcacagtttt--cctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
||| |||| | || | ||| | || || ||| || | |||| ||| | || ||| | || | | | | || | |||| |||||||| |||| |||||||||||| | || |||||||||||||| || || |||||||| ||||| |||||||||||||||||||| ||||| || || ||
gtttgctcatattggcatttcttcttgaattaagttttgaggtcctctatt--ttgtggattcgtttctttaacaaccttgctgatgacttatcttttca-cagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
-----gttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttat-taacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
| | || || | || || | | | || || | | |||| | | | | | | |||| | | | |||| |||||||||||||||||| | || |||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||
caggggctgttcttgaaatatgttgaaa----ggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
upper sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
gttatttcatttatgttttccaaatt-tgaggtttatattcttatatta-gctgttgggtcacagttttccttttt-attaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
|| | || || || ||| || |||||| | || |||| || | | | || | ||| || || || | |||| ||||||||||||||||| | | || |||||||| |||||||| || ||||||||||| || |||||||| || ||||||||| |||| ||||||||
gtcacca-atatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattagctgttgggtcacagttttcctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
tattaac putative branch site (score: 1)
ttttcctttttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA