Sequence
atgc intronic sequence ATGC exonic sequence...ttttgaaagaaatcaacaaattaagcagggaagtatgaacactcaaacgtggtcaataatttgttcatatgagttaaatttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
Basic information
species | Glycine max |
transcript | GLYMA05G08730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08730.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
---ttttgaaagaaatcaacaaattaagcagggaagtatgaacactcaaacgtggtcaataat--ttgttcatatgagttaaatttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
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aaacttcaagagtactgaacta-tgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgt----aatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA05G08730.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
---ttttgaaagaaatcaacaaattaagcagggaagtatgaacactcaaacgtggtcaataat--ttgttcatatgagttaaatttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
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aaacttcaagagtactgaacta-tgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtatt----ttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA05G08730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 5
ttttgaaagaaatcaacaaattaagcagggaagtatgaacactcaaa-cgtggtcaataatttgttcatatgagttaaa---tttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
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-cctgtaa--accctgcatgtcaaa-ggacatgtttcagagttaagagtacactgaaaaactgctgtaaactagcataacattcctttgtcctattcgatgcagGTGATGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACACAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: GLYMA05G08730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------ttttgaaag-aaatcaacaaattaagcagggaagtatgaa----cactcaaacgtggtcaata-----atttgttcatatgagttaaatttgtt-gtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
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gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAGMapped 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|51336549|gb|CO980415.1|CO980415EST: ATAGCAGCACACTTGCTTGTG GTGATGACTGTATCTCTATACAAACTGGTTNNNCGGACATATATGTACACA
genomic: ATAGCAGCACACTTGCTTGTGgtaagcataa ... aatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACA
EST:
gi|21677302|gb|BQ629653.1|BQ629653EST: CTTACAAAATTCTCAAAACGTGGTTATCTATAGCAGCACACTTGCTTGTG GTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACA
genomic: CTTACAAAATTCTCAAAACGTGGTTATCTATAGCAGCACACTTGCTTGTGgtaagcataa ... aatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgtggtcaataatttgttcatatgagttaaatttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
tactaaa putative branch site (score: 1)
aataatttgttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgaaagaaatcaacaaattaagcagggaagtatgaacactcaaacgtggtcaataatttgttcatatgagttaaatttgttgtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - -aaagaaa
- - - - - - - - - - - - - - - - - - - -cactcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgta