Sequence
atgc intronic sequence ATGC exonic sequence...gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA05G31670.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g36570.1 (Oryza sativa), 3'ss of exon 9
gtgaggaataatgaattttcaatttttcatattttatgattatccctc-aagaggtttgatttg-------atacttcttgtaactaat---atttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
| | || |||||| | | |||| ||| | |||| | | ||| | || ||| ||| ||| || || | | | | |||||||| ||||||||||| |||||||||||||| ||||| || | ||||| || || |||||||||||||||||
---------tttaatttctcaattcaatgcagct-gtgatgctccttttaagaagctacctttttaaaaataaacaacttttaaaaaatctaatatagatttctt-tacagCATCCAGGAAATATTGCTGTTGATGATGTCAACGGTGGGAGGCTTATCTTCTACGACTTTGGAATGATGGGAAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G040511_T02 (Zea mays), 3'ss of exon 9
---gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttgatacttcttgt-aactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
|||| ||| | | ||||| | | | | || ||||| | | | | || ||| || || | | | | |||||||| ||||| ||||| ||||||||||||||||| || ||| | ||||| ||||| || || |||||||||||
ttcatgagactgaatcatccctattgttttcttgctcctttttaatatctcaaa----taaagccgttgctctgtgttaaaagctaatggtgatttctttacagCATCCAGGAAACATTGCTGTTGATGATGTCAATGGAGGGAGACTTATCTTCTATGACTTCGGGATGATGGGAAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G64940.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgaggaataatgaattttcaatttttcatattttatg---attatccctcaagaggtttg---atttgatacttcttgtaactaatat--ttacac-tgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
| || | || | ||||| | | | || | ||| | | ||| | || || | || | ||||| | ||| | || ||||||| ||||| ||||| |||||||||||||||||||| || | |||| ||||| || |||||||||||||||||
----gtaagtctctatccttttttttttacactaagtgtcaacaatctttaatttggtgtaccaatacgaaaagactacaatctaatttgcttatgtatctttctgcagCACCCTGGGAATATAGCAGTTGATGATGTCAATGGCGGGCGGCTGATATTTTACGACTTTGGAATGATGGGAAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g01420.t01 (Vitis vinifera), 3'ss of exon 8
gtgaggaataatgaattttca-atttttcatattttatgattatccctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
|| || || || || ||| || | | ||| || || || | | |||| | | ||| | || || |||| | || ||||||||||||||||||||| || |||||||| ||||||||||| | |||||||||||||||||||||||||||||
gttgttcatgattcatccccacattatttagaatttctgctttgggttctataagtttcaatccataacttgcttagg-aacctttattttcttttggcagCATCCTGGAAATATTGCTGTGGATGATGTGAATGGTGGAAGGCTAATCTTTTATGATTTTGGAATGATGGGAAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S199_32V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgaggaataatgaattttcaatttttcatat---tttatgattatccctcaagaggtttgatttg-atacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
| | | | || | | |||| | ||||| | | | | ||| ||| | | | | | | | | | | || | ||||||| || ||||||||||| || |||||| ||| ||||| ||||||||||| ||||| |||||||||||||| ||
ctttgttttgttcaagtcttgcaccaaaatatcaatgtatgagtgttgaatgaaacgttctctttctagagtggctctgaacagtgtct----tgcttttgcagCACCCCGGAAATATTGCCGTCGATGATACCAACGGTGGCAGATTGATCTTCTATGACTTTGGAATGATGGGCAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttga---tacttcttgtaacta-atattta------cactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
|| | | | | || || | | | | | | | || || | ||||| || || | || | || | ||||||| || |||||||||||||||||||| | ||| ||||| ||||||||||||| ||||| || |||||||| ||
----------cctccttcttggtctatttatccttctggctgtacgtagaatgagatcatatggaccttcttctcatatctgcacgttgaatggctttttgcttctgcagCACCCAGGAAATATTGCAGTTGATGACGCCAACGGTGGGCGATTGATCTTTTACGATTTCGGGATGATGGGCAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ09480 (Selaginella moellendorffii), 3'ss of exon 10
gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
| | || | | | ||| | | | | ||| |||| | ||| || | ||||| ||| ||||||| ||||||||||| || || ||| |||| || ||| | ||||| |||||||||||||| |||||||||||
-----------------gtaagccctttttttctcttgagttttctggagaccttttcatttcttccttgttccttgtttcatttatgttgt------agCATCCAGGAAATATTGCTGTGGACGATTTCAACGGGGGACGCTTGATTTTTTATGATTTTGGTATGATGGGAAG
upper sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ35897 (Selaginella moellendorffii), 3'ss of exon 8
gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
| | || | | | ||| | | | | ||| |||| || ||||| || | | ||||| ||||||| ||||||||||| || || ||| |||| |||||| | |||||||||||||||||||| |||||||||||
-----------------gtaagccctttttttctcttgagttttctggagaccttttcattt---cctccttgttccttgtttcattcatgttc---tagCATCCAGGAAATATTGCTGTGGACGATTTCAACGGTGGACGCTTGATCTTTTATGATTTTGGTATGATGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
aactaat putative branch site (score: 2)
ttgtaactaatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggaataatgaattttcaatttttcatattttatgattatccctcaagaggtttgatttgatacttcttgtaactaatatttacactgttcgtgcagCATCCTGGAAATATTGCAGTTGATGATGTCAATGGTGGAAGATTGATCTTTTATGATTTTGGAATGATGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcttg