Sequence
atgc intronic sequence ATGC exonic sequence...cttatttccttatctattctaaaacctataatgcatgatgctatttttactgcttatcctaatactttttattttccctctcttggtggctttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTCTTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC
Basic information
species | Glycine max |
transcript | GLYMA02G02570.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 1
-------cttatttccttatctattctaaaacctataatgcatgatgctatttttactgcttatcctaatactttttattttccctctcttggtggctttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTC---TTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC---
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cagatggagcttttgcttttctttgttgagatc-atattgtcagaag--actctcttttgtcagtatgacatactaaaatatt---------gtaatttcatgt-aacagcagAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAGTCTCAGGTTCTACAACTACTAGTAATGCTGAAAGCAGTTCATCTGCATCTAA
upper sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G132184_T02 (Zea mays), 3'ss of exon 1
----------cttatttccttatctattctaaaacctataatgcatgatgctatttttactgcttatcctaatactttttattttccctctcttggtggctttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTC---TTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC
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gtgcagatggagcttttgcttttctttgttgagatc-atattgtcagaag--actctcttttgtcagtatgacatactaaaatatt---------gtaatttcatgt-aacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAGTCTCAGGTTCTACAACTACTAGTAATGCTGAAAGCAGTTCATCTGCATC
upper sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 1
cttatttccttatctattctaaaacctataatgcatgatgctatttttactgcttatcc-taatactttttattttccctctcttggtggctt---tccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTCTTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC---
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-----ggagccatgtttgaagatgtctgttctgcttaat-caatgtgaattttctttgtgtaatgttttacattctca-tatgttggttctatgtgtgggtcaacagAAAATAGATCTACAAATGATACAAGCAGAGACCAACCGGTTGCTCCAGTAGTCTCATCTACAACCACTAGTAATGCAGAAAGCAATTCATCCACTTCCAAMapped 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|207785452|gb|GD756977.1|GD756977EST: AGTGGCACCAGTACTCATTATG CTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAG
genomic: AGTGGCACCAGTACTCATTATGgtaaattcat ... tttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAG
EST:
gi|298170054|gb|HO018678.1|HO018678EST: ATCCAATGTTGATACCTCAGTCAGTGGCAGTGGCACCAGTACTCATTATG CTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAG
genomic: ATCCAAGGTTGATACCTCAGTCAGTGGCAGTGGCACCAGTACTCATTATGgtaaattcat ... tttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttactgcttatcctaatactttttattttccctctcttggtggctttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTCTTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC
tcctaat putative branch site (score: 2)
ctttccatt putative PPT
ttatcctaatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttatttccttatctattctaaaacctataatgcatgatgctatttttactgcttatcctaatactttttattttccctctcttggtggctttccattagCTGAAAGTAAATCAACTAATGATACTAGTAGAGACCAACCAACAGCCCCAGCAGTCTCTTCTACAACCACTAGTAATGCTGAAAGCAATTCATCATCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - - - -tactgct