Sequence
atgc intronic sequence ATGC exonic sequence...atagaaaaaacattttaagggaccaaatattatattgattcaattggttatgagtaggaacttgacacatttcctgcattacttgcattttgttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
Basic information
species | Glycine max |
transcript | GLYMA16G24670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24670.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g03400.2 (Oryza sativa), 3'ss of exon 2
atagaaaaaacattttaagggaccaaatattatattgattcaattggttatgagtaggaacttgacacatttcctgcattacttgcattttg--ttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
| | | | | | | | || ||| | | || ||| | | ||| | | |||||| ||| || |||| || |||||||| || || ||||| ||||||| | |||||||||||| |||||||| | | ||||| |||||||||||||| || ||||| ||||
-----gtgtataatctgaaa-atagcacttcatgttg--ttatttagtttcaaatgtgaaaacaa----------gtattactaaaattcgagattacacagGTTTTTGAAGGCAAGAAAGTTTGATGTTGAGAAGGCAAAGCAAATGTGGGCTGACATGTTGCGGTGGAGAAAGGAATTTGGTGCAGATACCATTCTTGAG
upper sequence: GLYMA16G24670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 2
atagaaaaaacattttaagggaccaaatattatattgattcaattggttatgagtaggaacttgacacatttcctgcattacttgcattttgttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
||| ||| | | | | | | || |||| || | | | || || ||| || |||||||| || |||||||| ||||||||| | || |||||||||||||||||||| | |||||||||||| |||||||||||||| | | |||
---------------------------gtctatcttggaatatatcatgccaatgtgcatctatgtccattattagcttgaatgtttcttcatttttcagGTTTTTGAAGGCTAGAAAATTTGATCTTGAGAAAACAAATCAAATGTGGTCTGACATGCTCCGATGGAGGAAGGAGTTTGGTGCTGACACAGTTATGGAG
upper sequence: GLYMA16G24670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g02400.t01 (Vitis vinifera), 3'ss of exon 1
-atagaaaaaacattttaagggaccaaatatta-tattgattcaattggtt-atgagtaggaactt-gacacatttcctgcattacttgcattttgttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
| || || || | || | | | || | ||| || ||| | ||| || | | |||| ||| || |||||| |||||||| ||||||||||| ||||||||| | || ||||||||| ||| |||||||||||||||||||| || ||||||||||| || | |||
ggcaattctaat-ttctactgttcctcacccaactgcggagaccattattttatgcttcatttctttaactagccttccaacgtactc---tttcgtaatccagATTTTTGAAGGCGAGGAAATTTGATCTTGAGAAAACAAAACAAATGTGGATTGATATGCTTCAATGGAGGAAGGACTTCGGTGCTGACACAATTATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttatgagtaggaacttgacacatttcctgcattacttgcattttgttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
acttgac putative branch site (score: 4)
ttttgtt putative PPT
attttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagaaaaaacattttaagggaccaaatattatattgattcaattggttatgagtaggaacttgacacatttcctgcattacttgcattttgttgaacagATTCTTGAAGGCCAGGAAATTTGACCTTGAGAAATCTAAGCAAATGTGGTCTGACATGCTTCAATGGAGGAAGGAATTTGGTGCTGACACCATCACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -gaaaaaa
- - - - - - - - - - - ccaaata
- - - - - - - - - - - - - - - - - - - - - - -ggttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt