Sequence
atgc intronic sequence ATGC exonic sequenceTGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtag
Basic information
species | Glycine max |
transcript | GLYMA08G13680.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 17
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaa---gttgagaaatttg-tattttttcagcattgttc--------tagtcaaagcttctgatatcctgcttcctttggccattttaaaa-catgtag
||| |||| ||| ||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||||| | |||||||||||||||||| | || |||| ||| | | ||| | |||| | | ||||| || | | ||| ||| | | | ||| |||| | | ||
TGGCTGCTCCATCATTAGCTGCTCATTCTCAGATGATAATAATGTTTATTATTGTGTGGGAACAGCATATGTTTTACCAGAGGAAAATGAACCATCAAAGgtaatatgtttggtagcttgatgttttcttacaggtgttcgatctcattaatagtattttcaaataaaaaaagttgtatttttgtttgaaaaataggaag
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G430027_T01 (Zea mays), 5'ss of exon 5
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgag-aaatttgtattttttcagcattgttctagtcaaa--gcttctgatatcctgcttccttt---ggccattttaaaacatgtag----------------------------------------------------------
||| |||| ||| |||||||| || || |||||||||||||| ||||||||||| |||||||||||||| | || || ||||||||||||||||| || | | || | | | ||| | | || ||||| || | || | ||| | || | ||| | ||||| || |
TGGCTGCTCCATCATTAGCTGTTCGTTTGTGGATGACAATAATGTCTATTACTGTGTGGGAACTGCATATGTTATACCTGAAGAAAATGAACCAACCAAGgtgatatatctgaaatcatgatcttttactaatg--ctagttaactcgtttttaata-cttgttcaatttacagcttgttttagttaatttctcagtgagccttttctatttctcgtgcacaaaatggttatgtatcggtacatcttgtag
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 17
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagt----tgagaaatttgtattttttcagcatt-----gttctagtcaaagcttctgatatcctg-----cttccttt--------ggccattttaaaacatgtag-------------------------------------------------------------------
||| |||| ||| |||||||| || || | ||||| | |||||| ||||||||||| |||||||||||||| | || || ||||||||||| || || ||| | ||| | | | ||| | | | |||| | || || | || ||| || ||||| | ||| |||| | |||||
TGGCTGCTCCATCATTAGCTGTTCGTTTGCGGATGATAGTAATGTTTATTACTGTGTGGGAACTGCATATGTTATACCTGAAGAAAATGAACCGACGAAGgtagtttatctgaaagcatgatgtttcactaatactagtcagttcccttttaatacgctaaaatactggttaactcccttttaatacttgtccaatttactgcttgtagtttatttctctgtgaaccttgtctatttctcgtgcacaaaatgcttatgtgttggcacatcttgtag
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 16
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtag--------
|||||| | || | |||||||| ||| | || || || ||||| |||||||| |||||||| |||||||| | || ||||||||||||||||| || ||| | | | | ||| || | || ||||| |||| | | | || || | || || | |
TGGTTGTTCAATTCTGAGCTGCTCATTCACCGAAGATAAAAATGTCTATTACTGCGTTGGAACCGCATATGTTTTACCGGAGGAAAATGAACCAACTAAGgtatctgttttctctgagaacatatcaacact-ctcagttcaaatattcttttctaatttgtctttgaaatacttatttttattttgtgatttag
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 17
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgta--agttgagaaatttgtattttt-tcagcattgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtag
|||||||| |||| | |||||||| || |||| ||||| ||||| ||||| |||||||| || |||||||| |||| ||||||||||||||||| || ||| | || || | | | | | ||||| || ||| || | | || | || ||| ||| ||||||
TGGTTGCTCCATATTGAGCTGCTCGTTTACAGACGACAAAAATGTCTATTATTGTGTTGGTACAGCATATGTTTTGCCCGAGGAAAATGAACCAACTAAGgtatcatttcagtgagactcactactgtttattttgtttgtgtgaaaatttatcttttcatttttatattg-----tttcgtggatgtag
upper sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 17
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtatttt--ttcagcattgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtag-----------
|||||||| || |||||||||||||||| ||||| | |||||| ||||| || ||||| || |||||||| | |||||||||||||| |||||||| |||| || | ||| ||| | | || ||| | | | || | | | | | || | | || ||||
TGGTTGCTCTATCCTTAGCTGCTCCTTCTCTGATGATAGTAATGTATATTATTGCGTTGGGACCGCATATGTTTTACCAGAGGAAAATGAGCCAACCAAGgtaaaatgccatattagtacatacatacatacctgtatatatgtattggtttgttgccagaatagcacttgcagtctaaattaatgtctgaatcgctgagMapped 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|24205748|gb|BU965001.1|BU965001EST: ACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAA GGAAGAATTATTGTTTTTGCTGTTGAAGATGGAAAACTACAGCTAATTGCC
genomic: ACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgag ... aaacatgtagGGAAGAATTATTGTTTTTGCTGTTGAAGATGGAAAACTACAGCTAATTGCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTTGCTTCATAATTAGCTGCTCCTTCTCAGATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA