Sequence
atgc intronic sequence ATGC exonic sequence...gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
Basic information
species | Glycine max |
transcript | GLYMA03G27460.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 5
gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
| || || ||| | || || | || | ||| ||||| | || || | | ||||||| ||| ||||| ||||||||||| | ||||||| |||||| || | ||||| | | || |||| |||||||| |||||||||||||||| ||| ||||||||
----------gtattat--gattgttttccaa-ctggtaatcaattttggttgccctgtaatttaatcg----ctggca--------ttacatttggcagGGGGTTGCTTTGTTGAAGGCAATTGGTTAAAAAATGCGTTCAGGTGGAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGGCACTATGGAGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
gtttgag---taagcatcatttgataataacgtgttcta-gtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|| |||| || || |||| ||| | || | | | | | | | || | | || || ||| || | ||| | |||| ||||| || || || || |||||||||||||| ||||| | |||| | |||| |||| |||||||| ||||| ||||| |||||||| ||||||||
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatgtcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 7
gtttgag---taagcatcatttgataataacgtgttctagtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|| |||| || | |||| ||| | || | | | | | | || | | || ||| || | ||| | |||| ||||| ||||| || || ||||||||||| || ||||| | |||| | |||| |||| |||||||| ||||| ||||| |||||||| ||||||||
gtatgagctatattttcccattgaaaatcaagt-tcttgatatgtacatatatgccagacatgtctgggataattgacttgatttacattcaaacaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 19
-----gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgta---actcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|| || || ||||| | | || | ||| |||| | | || | || | | | | | || | | | | | |||| ||||||||||| ||||| || ||| ||||||||||||| |||||| || ||| |||| |||||||| ||||| ||||| ||||| || ||||||||
gtatgcactgtgttttca-catttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 7
gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgta---actcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|| || || ||||| | | || | ||| |||| | | || | || | | | | | || | | | | | |||| ||||||||||| ||||| || ||| ||||||||||||| |||||| || ||| |||| |||||||| ||||| ||||| ||||| || ||||||||
--ctgtgttttca-catttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 6
--------------gtttgagtaagcatcat-ttgataataacgtgttctagtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgc----atagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
| | | | || |||| || ||| | | || | | | | | | ||| ||| || ||| | | | ||| | ||| |||| || || ||||| ||||| | |||||||||||||| ||| | |||| || |||| |||| |||||||| ||||||||||| ||||| || ||||||||
gtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgta-tatgatatattgcaatatat-taatacatttaaggataatggactagattgcatgatgctattgtagGAGGCTGCTTTGTAGAAGGTGGCTGGTTAAGAAATGCCTTTAGGTGGAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 7
-----gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgta---actcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|| || || ||||| | | || | ||| |||| | | || | ||| | | | | | || | | | | | |||| ||||||||||| ||||| || ||| ||||||||||||| |||||| || || |||| |||||||| ||||| ||||| ||||| || ||||||||
gtatgcactgtgttttca-catttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 6
gtttgagtaagcatcatt-tgataataacgtgttctagtttactcttctagtttgtatgtaactcaacta-acatctaggaatgt-tattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
|||| | | | ||| | | | | | | | | | || | ||||| || ||| | | || || | | || | ||| |||| || | || ||| | | || ||||||||||||| |||| | |||| ||||||||||||||||||||||| |||||| ||||| ||
gttt-atcatatttgattattcttacatcatatctggagtcaag-ttaaacactgtatctattgcaatggtatgtgtaagattctgtacctaccatgttttagGTGGCAACTATGCCATGGGAAATTATCTACGAAATGCATTTCGGTGGAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------gtttgagtaagcatcat-ttgataataacgtgttctagtttactcttctagtttgtatgt---------aactcaactaacatctaggaatgttattttacatt-----gcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
||| || || | | ||| | ||||| | | | | | ||| || | | |||| |||| | | | ||| |||| ||||||||||| || || ||||||||||| ||||| || || ||||||| | | || ||||| ||||| |||||||| || || ||||||||||||||
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaatatgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
upper sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
gtttgagtaagcatcatttgataataacgtgttctagttt-actcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
| | | |||| | | | || | | | || | | | | | || | | || | | |||| |||||||||| || ||||| |||||||| || |||||||||||||||||||| |||||| | |||| || ||||||||||||||||| |||||||||||||||||
-catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGMapped 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|21888705|gb|BQ741918.1|BQ741918EST: CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGG GCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAG
genomic: CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGGgtatgcataa ... cattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
aactaac putative branch site (score: 1)
aatgttattttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagtaagcatcatttgataataacgtgttctagtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA