Sequence
atgc intronic sequence ATGC exonic sequence...ttctatttcatgggatgaactgagatattgcttttgtgtttgtatgactttggagtttaactggtgtgttaaaatggcaatgtgtcttctttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
Basic information
species | Glycine max |
transcript | GLYMA07G02280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G02280.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g23180.1 (Oryza sativa), 3'ss of exon 4
ttctatttcatgggatgaactgagatattgcttttgtgtttgtatgactttggagtttaactggtgtgttaaaatggcaatgtgtc---ttctttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
| | ||| | || || | | | | | || | | | ||||| || | | |||| | |||| ||||| ||||||||| ||||| || ||||||||||| ||||||||||||||||| ||||| || |||||| | ||||| ||||| ||| |||| ||||||| || |||
---cactaaatgctactcacaatagaatcagtggtaaggctatttgtgatatgccataaactgacatgctgcctgccccatgtcttaatttctctttctgcagCTATGGTTATTCAAAAGAAAGATTTGTATGGTCCTTGATATCTGCAGTTGGAATATTTTGTTTGGGTTCAGGTGCTACCATTGTGCATGGAGTTCAAAAC
upper sequence: GLYMA07G02280.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G065839_T01 (Zea mays), 3'ss of exon 4
-ttctatttcatgggatgaactgagatattgcttttgtgtttgtatgactttggagtttaactggtgtgttaaaatggca-atgtgtcttct---ttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
| ||| ||| || | | | ||| | | | | || ||| | | || ||| || || || || |||| | || |||| | ||||||||| ||||| |||||||||||||| ||||| | |||||||| ||||| || ||||| | ||||| ||||| || |||| ||||||| || ||
ataatatc-cattagacaaccagtgatgggattaatat---tatacaactgcaatgat-gccttatgtcttgaattgacagatgttaatcctggcttttttgcagCTATGGTTATTCTAAGGAAAGATTTGTATGGTCTCTCATATCTGCAGTTGGAATATTTTGCTTGGGTTCCGGTGCTACAATTGTGCATGGAGTTCAAAAT
upper sequence: GLYMA07G02280.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G51610.1 (Arabidopsis thaliana), 3'ss of exon 4
ttctatttcatgggatgaactgagatattgcttt-tgtgtttgtatgactttggagtttaactggtgtgttaaaatggcaatgtgtcttctttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
| | | | | || ||| || | | | | |||| || || | || | | | | | ||| ||| |||||||||||| || || ||||||||||| ||||| ||||||||||||||||| |||||||| ||||| |||||||| ||| | ||||||||||||||||||
-gtgagtctctctagtaatcttgtatactgtatggtagaacagaacagctttct--cttgtttgaagaagtacttagacca-gccttttcactttgctcagCTATGGCTACTCAAAAGAAAGATTTGTATGGTCTTTGATATCTGCTGTTGGCATCTTTTGCCTTGGGTCTGGTGCTACCATAGTTAATGGAGTACAGAAC
upper sequence: GLYMA07G02280.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 4
ttctatttcatgggatgaactgagatattgcttttgtgtttgtatgactttggagtttaactggtgtgttaaaatggcaatgtgtcttctttt--tctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
| | |||| | | | || | || |||| | |||| | || | || || | ||| | | || || | ||| ||| ||||||||||| ||||||||||| |||||||| |||| ||||| ||||| || |||||||||||||||||||| || ||||| |||||||||| ||
ggcacatgcatgaaggatattcatattgaggcttacaacttgttt--cttttgttcatagactatatgaataatctgaaatttttatttttgtgttcttcagTTATGGCTATTCGAAGGAAAGATTCGTTTGGTCTCTGATTTCTGCCGTTGGTATATTTTGTCTTGGTTCTGGTGCTACAATTGTTCATGGAGTACAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactttggagtttaactggtgtgttaaaatggcaatgtgtcttctttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
gtttaac putative branch site (score: 3)
tgtgtcttctttttct putative PPT
tgttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctatttcatgggatgaactgagatattgcttttgtgtttgtatgactttggagtttaactggtgtgttaaaatggcaatgtgtcttctttttctacagCTATGGCTATTCCAAGGAAAGATTTGTTTGGTCCTTGATATCTGCTGTTGGGATCTTTTGTCTTGGTTCTGGTGCCACCGTTGTTAATGGAGTACAGAAC
- - - ttcatgg
- - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcaatg