Sequence
atgc intronic sequence ATGC exonic sequence...gtcataataactgcatgagcaacacattcttattttcgcaatagaacatgtattttgtggagacaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA02G35400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
----------------gtcataataactgcatgagcaacacattcttattttcgcaata-gaacatgtat-tttgtggagacaccaaaatgattattgatctaagttacttttaat--agATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
| | | | | || | | | | |||| | | | ||| | | | | | | ||| | || ||| || | ||||||||| || ||| | |||||| |||||||||| || ||||| |||||||||||||| || ||||| |||| ||| ||||| || || | | |||||
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
gtcataataactgcatgagcaacacattcttattttcgcaatagaacatgtattttgtggag-acaccaaaatgattattgatctaagttacttt-----taatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
| || || |||||| || |||| | || || | || | |||| || || | | ||||||||| |||||| | ||||| | ||||||||||||||||| || |||||||| ||| ||||| ||||| |||||||| || || || | |||||
--------------gtaagtaaacttgtcttat----agaaaagaatagaaataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcataataactgcatgagcaa-cacattcttattttcgcaatagaacatgtattttgtggagacaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
||| || ||| | | | || ||| ||| | | | || ||| | | | || ||| | | | | || ||||||||||| | || || |||||| | ||||||||||||||| | | ||||||||||| || |||||||||||||||| |||||||| ||| || ||
---gtaagtacaccatcatctatcagtcccttgtttctatagaaaggaacaaatcttgatgtg---------ttttttttgtttt---tgatttgatatagATGATACTGGGATTCTCTGGGGAATAAAGTTCTACAATGATCTGTTGATGCAAGCTGGGCCATTTGGTAATGTACAATCTGAGCTACTTTTCCAGAAAGA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 5
--gtcataataactgcatgagcaacacattcttattttcgcaatagaacatgtattttgtggagacaccaaaatgattattg-atctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
|||| ||||||| ||| | | | | ||| | | | | | | | || | || ||| ||| | | || | || ||||||||| || ||||| ||||| ||||||||||||||||| | ||| ||||||||||||||||||| |||||||| ||||||||||| || | |||||
atatcatcgct-ttgcatga-caaaatgtgcatgtttcc-ctttttggtttatgacatattgaaaattgaacatgggtataacaagttcttttttcccaacagATGATACTGCCATGCTATGGGGGGTTAAGTTCTACAATGATCTGCTCGTGCAAGCTGGCCCTCTTGGAAATGTACAGTCAGAGCTACTCTTTCGGAAGGA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 5
------------gtcataataactgcatgagcaa------cacattcttattttcgcaatagaacatgtat-----tttgtggagacaccaaaatgattattgatctaagttactttta-atagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
|| || | || | |||| | | ||| |||| || | | || || | | || || || | || | | || ||| | |||||| || || ||| | |||||| | ||||| ||||||||||| ||| |||||||| |||||||| ||||| || |||||||||||||| |||||||
gtacgtcatatcttctcaagatttggttttgcaaagttgttgtctgccagctttttaaataaaaaacatgcaactgttcgtcttaatcctaacatc-ttgtgaatatgaattttggttatacagATGACACTGCCATGTTATGGGGAGTCAAGTTTTACAATGATTTGCTCTCTCAAGCTGGTCCTCTTGGGAATGTGCAGTCAGAGCTACTATTTCGAAAGGAMapped 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|298185762|gb|HO028073.1|HO028073EST: CCAACTTTTCAGTTTCAACTACAAAGCAATAACTCCCTACGGGTCAATAA ATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGC
genomic: CCAACTTTTCAGTTTCAACTACAAAGCAATAACTCCCTACGGGTCAATAAgtaagtgtga ... cttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgtattttgtggagacaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
tattgat putative branch site (score: 3)
ttactttt putative PPT
taagttacttttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcataataactgcatgagcaacacattcttattttcgcaatagaacatgtattttgtggagacaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - -tgcatga
- - - - - - - - - - aacacat
- - - - - - - - - - - - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaaa