Sequence
atgc intronic sequence ATGC exonic sequencegttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
Basic information
species | Glycine max |
transcript | GLYMA09G04820.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04820.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 1
---------------gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttgg--ttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
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gtaagaaccttatgcccttgctctcgctctgccttcttcctgcg-ctcgatttggtttccgtcgctccccttgttgaccggttcttcgttgggaatgggatttggccatttggggacttttctgtcgattccttctctg-tcggtcagGCATTCGAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCA
upper sequence: GLYMA09G04820.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgtt----cagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
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-------------------------------aatcaattggttcaactaagagtctggtgaattgtctatggagt-gattatatgtg-tactctgatagataaggatttg--cattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
upper sequence: GLYMA09G04820.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgt--tcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
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gttggcttt-----ctttctctctcaatttctttggctt---aggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAMapped 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|207706557|gb|GD688505.1|GD688505EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCCgttagtttta ... gattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
EST:
gi|208035139|gb|GD835497.1|GD835497EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCCgttagtttta ... gattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
EST:
gi|207700310|gb|GD682647.1|GD682647EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC GCGTTTGAGAAGTACAATGTGGAG
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCCgttagtttta ... gattgttcagGCGTTTGAGAAGTACAATGTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
tcttgac putative branch site (score: 3)
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgttcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG