Sequence
atgc intronic sequence ATGC exonic sequence...atctgagccatatttcctattttctttcacctataatttataattttttatatctcaaattaacaatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
Basic information
species | Glycine max |
transcript | GLYMA02G03750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 5
atctgagccatatttcctattttctttcacctataatttataattttttatatctcaaattaacaattt-----ggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
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-----ataagcataagcgaattaatgaggccctaaatatctatttctgcttatatcacatttgagattttattaaattttttatttgtttgaattgtgtttctagGTTGAAATCATTAATGAGTTGCCTGAAGACAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTT
upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------atctgagccatatttc-ctattttct-ttcacctataatttataattttttatatctcaaattaa----caatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
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gtgggttaagctgtgtataaatatcattggattgtgttatgctcaccta-accttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaat-catgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 5
--------------------atctgagccatatttcct-attttctttcacctataatttataattttttatatctcaaattaacaatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
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gtgagtgaagctccatttttatatcatccataccatttgagctatccttagctact-tccttattttcttactactcttattgttactcatatgggttgtttat-catatctcataatcagATTGAAATCATCAATGACTTACCCGAAGACAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGACCCCATATACCAAATACAT
upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 5
----------------atctgagccatatttcctattttctttcacctataa-----tttataattttttatatctcaaattaacaatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
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gtaagtgaagctccatttttatatcatccacaccatttgaccccatccttagccacttccttattttcttactattctgatcctcactcatatgggttgtttat-catctcccttaatcagATTGAAATCATCAATGACTTACCTGAAGACAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGGCCCCATATACCAAATACATMapped 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|22540425|gb|BU090268.1|BU090268EST: AAGTTACACGTGATCAGGCACTTGAGATGTTTTCAGATTATAAGTTTAAG GTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGA
genomic: AAGTTACACGTGATCAGGCACTTGAGATGTTTTCAGATAATAAGTTTAAGgcaagtatag ... ttgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGA
EST:
gi|193656382|gb|FK602854.1|FK602854EST: AAGTTACACGTGATCAGGCACTTGAGATGTTTTCAGATAATAAGTTTAAG GTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGA
genomic: AAGTTACACGTGATCAGGCACTTGAGATGTTTTCAGATAATAAGTTTAAGgcaagtatag ... ttgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatatctcaaattaacaatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
aattaac putative branch site (score: 2)
tcaaattaacaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctgagccatatttcctattttctttcacctataatttataattttttatatctcaaattaacaatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT
- - - - - - - - - - - -ctttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtgg