Sequence
atgc intronic sequence ATGC exonic sequence...actaccttgaatcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
Basic information
species | Glycine max |
transcript | GLYMA03G40330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 3
actaccttgaatcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgc--ttctcttctacattttgt--agTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
|| || || | || ||||||| ||| || | | || || || || ||||| || | |||| | | | |||||||||| || ||||||||||| ||||| || || ||||||||| |||||| |||||||| ||||||||||| |||||| | ||||| ||| |||
gataatgtgtgaagtagatctgt-ttattgtcatctttgttgaaattatgtagcattg---ttttacacttttactaaagaattgcttattacaatctatgcagTTCTTTACAACTGAACCTTATGCATGTGAACCATCAAGTCTCCCAGCATATCCTCCAAGCAAAGAAATGGATGCAAAACGAAGAGATGAAGAAGCCAGAC
upper sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 4
-actaccttgaatcttatttaggtgttattgttgagttttg----acaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
| ||| || || || | || | ||| ||||| | | | ||||| || ||| ||| || || ||||| | | |||||||||| || ||||||| ||| ||||| || || ||||| ||||||||||| |||||||| ||||| |||| ||| || | || || ||| |||
tagcacccagattcccatctttgtcacacatttggtttttgtagcatattttttttggtattg----tgtattcatgccttctgtttactttctatggat-gcagTTCTTTACAACTGAACCTTTTGCATGTGAACCATCGAGTCTTCCAAAATATCCTCCAAGCAAAGAAATAGATGTGAAAAGAAGAGACGAAGAAGCCAGAC
upper sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 4
actaccttgaatcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttg----tagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
|||| || | | || | | ||| | | | | | | | || | || ||| | | | || | | | | || ||||| ||| | || || |||||||||||| | ||||| ||||| |||| |||||| ||||||||||| |||||||| || | | || || || ||||
-tggccttatgcatttat--gctgcttgtaatgaactattattccgtcataactaccagttactcat-catgtgctcttttttttattaaaaaaatggacttagTTTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAA
upper sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
--------actaccttga-atcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
|||| || | | ||||| | || | ||| | || | ||||| ||| | | |||||| | | | || ||| | || || ||||||| || || |||||||||||||||| || ||||| || || ||||||| ||||||||||| |||||||| || | || ||||||||| |||
ggagttctactaggctggcaattcatttaaat-ttctagtta---taagatacccttttgaaattttag--catatatactcatttt---ctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|23064160|gb|BU578933.1|BU578933EST: CAATTGATCCAGTAGAACGGAAAACTGCCTCAGATGCTCTAAGAAGTGAG TTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATAT
genomic: CAATTGATCCAGTAGAACGGAAAACTGCCTCAGATGCTCTAAGAAGTGAGgtgggatttt ... cattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
ccttgcttctcttcta CT-rich tract
atatacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaccttgaatcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - ccttgaa
- - - - - - - - - - ggtgtta
- - - - - - - - - - - - - - tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaacc