Sequence
atgc intronic sequence ATGC exonic sequence...aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
Basic information
species | Glycine max |
transcript | GLYMA01G37120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G37120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 2
aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
||| | || || | | | | ||| || | ||| | | | || || | || ||||||||||| ||||| ||||||||||| || |||||||| || ||||||||||| |||| |||| | || || || || ||||| ||||| || | |
----------------gtga-gtactacggccacactgtatccttggtgatt-ttgttttagatcatgcatctctta--ggcaatgtgaacttg---cagTATCTGAGCAATGGGAGGTTCAAGAACGCGGATCACCAGGCGGTGGTGAACTCCGACTGCTGCCGGCTGTCGATCGCGACGTTCCAGAACCCGGCGCCGG
upper sequence: GLYMA01G37120.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
---aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
| || | ||||||||| | ||||||| ||||| | | | | ||| | | ||| | | | | | | ||||| ||| | |||| ||||| |||||||||||||||||||| || || ||||||||||| | || ||| | ||||||||||||| ||||| ||||| || | |
gttagtactctatccatttat------tggcttttttg-tttctctgtttttggttttga-----cttggtcaatct-------tgatttgtct-tgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
upper sequence: GLYMA01G37120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g14310.t01 (Vitis vinifera), 3'ss of exon 2
aatatttcttccatttatgatatttaactt-tttttctttctacctatctattactgag-----agaattcaattaatttatgcgggtaacatatttgtg-atgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
| | |||| | ||| || ||||| | | || | | | ||| |||||||| | | | | ||| | |||||||||||| ||||| |||||||| ||||| || |||||||| ||||||||||| |||||| || | || || ||||| ||||| |||||||| | ||
---------gtgagtagtgattctctgcttattcctcttttggattccccatcgaaggggcagaataatataattaattaactctg-cattcgattgacgtgggcagTATCTGAGCAATGGGAGGTTCAAAAATGCGGACCACCAAGCTGTGGTGAACTCCGACTGCAGTCGGTTGTCGATTGCCACGTTCCAGAACCCAGCCCCAG
upper sequence: GLYMA01G37120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 2
aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatt--tgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
|| | ||| | ||| | | | | | | || || || ||| | | | | | | || || | || ||||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||| | ||| | | |||||||| |||||||||||||| |||| |
tatgtggtcaacatccacaatagtccttcctgatatggtattcaaattcat-gctacccgaacccgaaagagaga-gtgattattggtttggtatggtgcagTATCTGAGCAATGGGAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCCAATCATAGCAGACTGTCCATAGCAACATTCCAAAACCCCGCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
gggtaac putative branch site (score: 3)
agaattcaattaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - -ttcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - -tactgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttatgc