Sequence
atgc intronic sequence ATGC exonic sequence...tcttgcacaataaaatatgttaacatggttgaggttaaaaggatgtttatacagccttttctttaggccatgcctgaacttctaaacgtcttatatgcagAATGGGAAGGTTCCCCCCAGTAGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAGCATATAGTCCTTTCTTGTAATGCCACATCTGATCATGCCATC
Basic information
species | Glycine max |
transcript | GLYMA09G25180.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G25180.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g39580.1 (Oryza sativa), 3'ss of exon 1
tcttgcacaataaaatatgttaacatggttgaggttaaaaggatgtttatacagccttttctttaggccatg--cctgaacttctaaacgtcttatatgcagAATGGGAAGGTTCCCCCCAGTAGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAGCATATAGTCCTTTCTTGTAATGCCACATCTGATCATGCCATC
| | || || | | || | || || || ||| | | || |||| || |||| | | ||| || | | ||| ||||| | ||||||||| |||| ||||| ||||| || ||||| || |||||||||||||| ||||| || ||||||||| || ||||||||
tgataatttattaa-tgttttgtcttg-ttcagattactactcttttgttacaatagagatttccaagcatgatcataaacgaacttgttcctgaattccagGTGTGGAAGATACCCCCCAGTGGTGAAAACAGCTGTGCCTGTGGATGGTAGATTTGAGCATATAGTTCTTTCCTGCAATGCCACAATGGACCATGCCATT
upper sequence: GLYMA09G25180.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g00620.t01 (Vitis vinifera), 3'ss of exon 3
---tcttgca-caataaaatatgttaacatggttgaggttaaaaggatgtttatacagccttttctttaggccatgcctgaacttctaaacgtcttatatgcagAATGGGAAGGTTCCCCCCAGTAGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAGCATATAGTCCTTTCTTGTAATGCCACATCTGATCATGCCATC
| || ||| || ||||||| | || | | | |||| || || | | | | || | || | | | | | || | |||| |||||||| || ||||| || |||||||||||||| || |||||||| |||||||||| ||| || ||||||||||||||||| ||||| ||||| |||
aactattaagtcaaaaagatatgttgatcaattttaaggtggcaggaaactt-tagactttgataactgggaaggacatgtatta--acatattttgtg-gcagGATGGGAAGATTTCCCCCGGTTGTGAGGACAGCAGTACCTGTAGATGGGAGGTTTGAGCGTATTGTTCTTTCTTGTAATGCCACTTCTGACCATGCTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatacagccttttctttaggccatgcctgaacttctaaacgtcttatatgcagAATGGGAAGGTTCCCCCCAGTAGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAGCATATAGTCCTTTCTTGTAATGCCACATCTGATCATGCCATC
ttctaaa putative branch site (score: 2)
ttttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgcacaataaaatatgttaacatggttgaggttaaaaggatgtttatacagccttttctttaggccatgcctgaacttctaaacgtcttatatgcagAATGGGAAGGTTCCCCCCAGTAGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAGCATATAGTCCTTTCTTGTAATGCCACATCTGATCATGCCATC
-cttgcac
- - - - aataaaa
- - - - - - - - - - - - - -gttgagg
- - - - - - - - - - - - - - - - - - - - ggatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcct