Sequence
atgc intronic sequence ATGC exonic sequence...taaattgtaatgtatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
Basic information
| species | Glycine max |
| transcript | GLYMA09G39750.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------taaattg-taatgtatttctactacattgacta---tagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
|| ||| | ||| || | | || || ||| | || |||| | ||| | | | ||||| ||| || || || | | | |||||||||||| ||||||| || ||||| | ||| ||| || |||| ||||||||||||||||| |||||||||| || || |||||||| || ||||||
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaac-aaactacattattctcttcttg-cagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
upper sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------taaattgtaat---gtatttctactacattgactatagacg-------aagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
| ||| | || || || | ||| || || | | | || || ||||| || || || || | | ||| | | | | |||| | |||||||||||| ||||||| |||||||| | ||| ||| || |||| ||||||||||||||||| |||||||||| || || ||||||||||| ||||||
gtaagattacaattcaatggttgtttcgaactatggatacttgttgaatcctgatcatgtggttgtgctat-ttaccttttggtgcttgtataaattatttgatctcaaaacgtgtgcttgttaag--aaactgtgtcgttttattattg-cagGGATAGAGACCGATATGTCCAAGGAGATTACCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAGAAGGAAATG
upper sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------taaattgtaatg-tatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
| | || ||| ||||| | || | || | | || ||||| || || || || | | ||| | | | || |||| | |||||||||||| ||||||| |||||||| | || ||| || |||| ||||||||||||||||| |||||||||| || || |||||||| || ||||||
gtaagattacaattcaatggttgtttccaactatcgatacttgttgaatcctgatcatgtggtcatgctatttaccttttggtgcttgtata---aattatttgatctcaaaacgtatgcttgttaag--aaactgtgtcattttattattg-cagGGATAGAGACCGATATGTCCAAGGAGATTATCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAAAAGGAAATG
upper sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
taaattgtaatgtatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
|||| ||||| |||| | || | || | ||| | || || || | | || | | || ||| |||||||| ||||| ||||||| |||||||| | ||| ||| || |||| ||||| || |||||| |||| ||||| || ||||||||||| |||||| |
------gtaagctattt-----acatgaataatgttgtttatcagttcttctaaaactcttaacttaat---cccagtttt-caactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
upper sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 4
taaattgtaatg-tatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttat--cgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
| || |||| | | || | || | || | || | || | || | | |||| | | | | | | | || | | | ||||||||||||| | ||||| |||||||||| ||| || || |||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||
-atatctcaatgatgctgatattgca--aatgatttccatttttccaagagtatgtattctatagcttataatgtgattcgtcttgttttctaacaactccagGGATAGAGATCGGTATGTACAAGGAGACTACCGTTTCAGACATGGATACTGCAAGCACAATCCTAGGAAAATGGTAAAGACATGGGCTGAGAAAGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
aactaaa putative branch site (score: 2)
tcttatc putative PPT
ttttatgaactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaattgtaatgtatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - ctacatt
