Sequence
atgc intronic sequence ATGC exonic sequence...agaaaaagggattgcaatttctatttttattcgaattcttcctttctattttcaattatcaacttttttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
Basic information
species | Glycine max |
transcript | GLYMA02G16860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
agaaaaagggattgcaatt--tctatttttattcgaat---tcttcctttctattttcaattatcaacttttttttttaatttc-atttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
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gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
upper sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G020574_T07 (Zea mays), 3'ss of exon 6
--------agaaaaagggattgcaatttctatttttattcgaattcttcctttc-tattttcaattatcaacttttttt-tttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG-------------
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gtattatttctattatccattggtatgtgctgtgttgcattagtttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacaggccattaaagatgatgttggaactattcgaattcagCGACCGCACAAAGGACCCTTTTATGCATCATCAAAGAGCATTGATCAACTTATTGTGAATCTTGGGAAATGGGCCAA
upper sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G020574_T08 (Zea mays), 3'ss of exon 6
--------agaaaaagggattgcaatttctatttttattcgaattcttcctttc-tattttcaattatcaacttttttt-tttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
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gtattatttctattatccattggtatgtgctgtgttgcattagtttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCGCACAAAGGACCCTTTTATGCATCATCAAAGAGCATTGATCAACTTATTGTGAATCTTG
upper sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G873779_T01 (Zea mays), 3'ss of exon 2
--------agaaaaagggattgcaatttctatttttattcgaattcttcctttc-tattttcaattatcaacttttttt-tttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
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gtattatttctattatccattggtatgtgctgtgttgcattagtttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCGCACAAA----------------------------------------------------
upper sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 6
--agaaaaagggattgcaatttctatttttattcgaattcttcctttctattttcaattatcaactttt---ttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
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cttgtatgaggag-----atctatatgattgatcaggtagttttgattgaataccccttttttttttgcaaatcttatatacgtgtttctttaatatatgatcagGCTATCAAAGATGATGTTGGAACAATTCGTATTCAGCGGCCCCATAAAGGACCATTTTATGTCTCTCCCAAAAGTATTGATCATCTTGTTGCAAATCTTGMapped 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|192326738|gb|FK018895.1|FK018895EST: GAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAG GCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGG
genomic: GAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAGgtaatgtaat ... gtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGG
EST:
gi|192323713|gb|FK016019.1|FK016019EST: GAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAG GCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGG
genomic: GAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAGgtaatgtaat ... gtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattttcaattatcaacttttttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
ttttaat putative branch site (score: 3)
ttcaattatcaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaaaagggattgcaatttctatttttattcgaattcttcctttctattttcaattatcaacttttttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG
agaaaaa
- - - -gggattg
- - - - - - - - - - - - - - - - - -ttcttcc