Sequence
atgc intronic sequence ATGC exonic sequencegtataatatatcagtatgaataatgataacacaaatttgttaaatatgttgatttcattatatattacaaaccaatgattattatattcttgaaatcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
Basic information
species | Glycine max |
transcript | GLYMA04G06910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgt-tgatttcattatatattacaaaccaatgatt-attatattcttgaaa--tcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
|||| | | | | ||| | |||| || ||| | | || | | | | || | ||| ||| ||| || | | | | |||| | ||||||| | | | | |||| | ||| | ||| ||| ||||||| |||||||||| |||||| || || ||||| |||||||| || || ||||| || ||||||||||| ||||||||| ||| | ||
gtatgtcttgttctca-atttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaatta--gctgatttt--atgtt--tctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
upper sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G002851_T01 (Zea mays), 3'ss of exon 4
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgttgatttcattatatattacaaaccaatgattattatattcttgaaatcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
|||| | | |||| | | | | ||| ||| | | |||| |||| || | |||||||||| | |||| | | | || | | |||||| | ||||| |||||||||| ||||| || || ||||| || ||||| || || ||||| || ||||||||||||||||||||| |||| | |||
----------------------------gtacaaccgtacaagatatcccaaatgc-tagtatgcaaca---ccttttgtattctatttctgtggaaatgatttagttcaatag-----caat-tagttatttcacattga-ctgcagGCCGCAAAAGATGGGGAGCCATGGTGGGATAGCCCATGGGGCCCAGGAAGGCCAGGATGGCACATAGAATGCAGTGCCATGAGTGCACATTATTTGGGTC
upper sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156565_T01 (Zea mays), 3'ss of exon 4
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgttga-tttcattatatattacaaaccaatgattattatattcttgaaatcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
| | || | | | | ||||| | | || | |||| ||||| || | |||| |||||| | |||| | | || ||| || |||||| ||||||| |||||||||| ||||| || || ||||| || ||||| || || ||||| || ||||||||||||||||||||| |||| | |||
------------------------------------gtacaagatgtcccaaatcttattatgca----acacttttttgtattctattcctgtggaaatgatttcgttcagcag-----caattagtttatttcatgttaa-ctgcagGCTGCAAAAGATGGGGAGCCATGGTGGGATAGCCCATGGGGCCCAGGAAGGCCAGGATGGCACATAGAATGCAGTGCCATGAGTGCACATTATTTGGGTC
upper sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g06470.t01 (Vitis vinifera), 3'ss of exon 4
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgttgatttcattatatattacaaaccaatgattattatattcttgaa-atcttaatttagttcagaacttactc--aatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
|| || || ||| | | | | |||| ||||| | | || ||| | ||| | || | || ||| || || | ||||| |||||||| ||||| || |||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| |||||||| ||||
------------------------------------------------tta--ttagttggatagcaaatgttatttgttatcatatttccaactgtatttgtttgctattgaagtaccttttgctacagaatct-attggtaatttgcagGCTGCAAAGAAGGGGGAACCCTTTTGGGACAGTCCATGGGGGCCTGGGAGACCTGGATGGCATATTGAGTGCAGTGCCATGAGTGCTGCTTATCTGGGTT
upper sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S504_12V6.1 (Physcomitrella patens), 3'ss of exon 4
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgttgatttcattatatattacaaaccaatgattattatattcttgaaatcttaatttagttcagaacttactcaatgtgga--ttcttgatgctattct---gcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
| | | | |||| | | | ||| | || | || ||| || | || | | | | | || | | | || | || | || || ||| | || | | || | ||| | |||| ||| || || || ||||| |||||| ||||| ||||||||||| | || || ||||| |||||||||||||| |||||||| | || | |||
------gtcagcgcccttgaaaatggtgagagaaaactcttctgtctgctgagttaggt-cctagggaattagactaaatcttgtcctactaaagtgggtgttggttctcaaattttctctctctgaaggtcgctggtatcattttctcgcagAGTGCGAAACCCGGAGAGCCTGCTTGGGACAGTCCTTGGGGTCCTGGGCGCCCGGGCTGGCACATTGAATGCAGTGCTATGAGTGCGGAGCATTTAGGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
ctattct CT-rich tract
taatttagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgttgatttcattatatattacaaaccaatgattattatattcttgaaatcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT