Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
Basic information
species | Glycine max |
transcript | GLYMA15G04830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
||| ||| || | || || || | | ||| | |||| ||||| | | | || ||| | | || | ||| || ||||||||||||| | || |||||| | || || || ||||| || ||||| || || |||||||||||||||||||| ||||| | | ||| |||||||
gtaattctaaggacag--tgtcctggcagattt-gattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgtt---ccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
upper sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
| ||| | | || | | ||| |||| | | || || || || | | ||||| || || |||||||||| ||| | || || ||| |||||||||| ||||| || ||||| || || ||||||||||| |||||||| ||||| | | ||| |||||||
------------gtaaccctaagaat-ggcccttgacagc-tttgattttagtaacacgttgctcaatg--atggtttatgtgtatctatttgtt---tcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
upper sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 6
gtatgagtaactgcaacttttcttgtcaattctcaatttcatttttttttt-attattttctgagtgattttattattaagatatatcttattatt----atatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
|||||| | || | | || |||| | | | ||| | ||| ||| | || || ||| | || | ||| ||||||| |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||| |||||||
gtatgaactgc-ataattagttcagtaaattattattggcatatgaggtttgattttgaacttagaaattgaggtgaggtaattaaaaagattgcctgaaatatcagGGATAGCAAATTAACAAGGTTATTGAGGGATTCCTTGGGAGGGAAAACAAAAACATGCATAATTGCCACAATATCGCCCTCCATTCACTGCTTGGAAGAG
upper sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S13_177V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatat-----cagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
| |||| || | || | || | | ||| | || ||| | || | || | | | | ||| ||| | | |||| | ||| |||||||||||| | || |||||||| |||||||||||||| || || || || || |||||||||||||| | || || ||| |||| || || ||||||
gtaatttgtcctctgttgtgactatttgctggagtgacaaattccttcccagttttgtgttgattataattgtttctatttctattttca---actgtatgcctaatgtttctcttgacttcgtatggatacagAGATAGCAAGCTGACAAGATTGTTAAGGGATTCTTTGGGAGGAAAGACAAAGACCTGCATTATTGCCACCGTTTCGCCCTCCGTTCATTGCCTTGAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
tgagtgattttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA