Sequence
atgc intronic sequence ATGC exonic sequencegtttcatagtccttttaaatatgtgattgtaatggctaggaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
Basic information
species | Glycine max |
transcript | GLYMA10G33040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
--------gtttcatagtccttttaaatatgtgattgtaatggctag-gaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
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gtgccccatgctcacaattacctgacctttttatttttcttaccaagtgaattgatttatcagttattcttgccttgttggaatt--cagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA
upper sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
gtttcatagtccttttaaata-tgtgattgtaatggctaggaatcaaaatgta-caatgttctgattatattgg----gtgtta----cagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
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--gttgctgtgctctgaaagagtgtgacc-tacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
upper sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatagtccttttaaatatg-tgattgtaatggctaggaatcaaaatgtacaatgttc--tgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
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------------------gtatgatgctcgtgagttctttctttctcgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
upper sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatagtccttttaaata-tgtgattgtaatggctaggaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
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---gtatgatgctcgtgagttctttctttattgttgctttgagcc--------ccatgtc-----tgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGAMapped 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|254344265|gb|GR851068.1|GR851068EST: TTCAGAAGCATGATCTTGATTTGATTTGCA-GGCGCATCAG GTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATC
genomic: TTCAGAAGCATGATCTTGATTTGATTTGCAGGGCGCATCAGgtttcatagt ... ggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATC
EST:
gi|254318435|gb|GR832603.1|GR832603EST: AGAATTCCTTCAGAAGCATGATCTTGATTTGATTTGCAGGGCGCATCAG GTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATC
genomic: AGAATTCCTTCAGAAGCATGATCTTGATTTGATTTGCAGGGCGCATCAGgtttcatagt ... ggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtaatggctaggaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
ttctgat putative branch site (score: 3)
tgattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcatagtccttttaaatatgtgattgtaatggctaggaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG