Sequence
atgc intronic sequence ATGC exonic sequence...gcattattagcattacatttagttttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
Basic information
species | Glycine max |
transcript | GLYMA11G01190.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
----gcattattagcattacatttagttttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
|| || ||| | | | || ||| || || || ||| ||| || | | | | | | | | || | | ||||| || ||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| | || || || | || | ||||| || ||||| |
tcacatatgatctgcactctactggcaattgg-aagatg--ctattttctcagcaaacaatttatattgcaccctaac-gatgtcatctgtgcctttttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
gcattattagcattacatttagtt--ttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| | ||| | || || | || | ||| | ||||| || ||| | ||| | | | | ||| | | || | | ||||| || ||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| ||||||| || | || | ||||| || ||||| |
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaac--gatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
-gcat-tattagcattacat-ttagttt--tatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| | || | || || || | || ||| ||| | ||| | ||| | || || || || | | ||| | || || |||||| ||||| ||||| ||||| || ||||| |||||||| || || ||||||||||| |||| ||| | |||| ||||| |||| ||| |||
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagta-acttcttgcggttgatgactgttccattctccatgcttctttttttca----gGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
upper sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
gcattattagcattacatttagtttta---tcaagctggattagttgtacagttcacacatttttcttctcttaatt-tgttactccttttga---ttgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| || || || | | | || |||||| || || |||||| |||| || || || || || | | || ||| |||||||||||||| ||||| || || ||||||||||||||||||||||||||| | ||||| ||||||||| | || ||||| ||| | ||| ||
----tgttggcttttcttcttcccctaaattcaagcaacatcgttt---cagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
upper sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
-----gcattattagcattacatttagttttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
||| | ||| || | | |||| | || || || | | || | ||| || ||| || || | || | | ||||||||| || || ||||| || ||||| || ||||||||||||||||| || ||| |||||||| ||||||| ||||| || ||||| |||||||| |||||
atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaa---acttagtttctaaggggtagtttttttcttcactttaat--caaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
gattgac putative branch site (score: 3)
ttaatttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattattagcattacatttagttttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - -gcattac
- - - - - - - - - - - - - - caagctg
- - - - - - - - - - - - - - - - - - - - - - - - - tcacaca