Sequence
atgc intronic sequence ATGC exonic sequencegtacactttcatcattatggtaactatgtcacaagtactttttttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
Basic information
species | Glycine max |
transcript | GLYMA16G28900.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
---------------------------gtacactttcatcattatggtaactatgtcaca-agtactttt--tttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
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gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
upper sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g37580.1 (Oryza sativa), 3'ss of exon 10
-------gtacacttt-catcattatggt-aactatgt-cacaagtactttttttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
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gtatgtgtttcacctcacgtcctcattctcagttctgtgtataaacagtttcatttttg--taatgcatttcctttatttgtt------tagTTGTGGAAGGAGGATCAAACTGGAGCATGGGCCAAAGGCAGCTACTTTGCTTGGGCCGTGCCCTCCTGCGACGAAGCCGCATCTTGATCCTTGACGAGGC
upper sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
-gtacactttcatcattatggtaacta-tgtcacaagtactttttttcctagttgataaa-----------aact-----agtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
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atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
upper sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
---gtacactttcatca-ttatggtaactatgtcacaagtactttttttcctagttgataaaaactagtaatatgttgttac--atagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
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gtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGCMapped 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|192296255|gb|FG992271.1|FG992271EST: TCAATTGCGAGAAGCTGTCCAAGAGAAAGAAGAGGGCCTGAACTCCCCAG TTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTT
genomic: TCAATTGCGAGAAGCTGTCCAAGAGAAAGAAGAGGGCCTGAACTCCCCAGgtacactttc ... tgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTT
EST:
gi|10843700|gb|BF066974.1|BF066974EST: GAACTCCCCAG TTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTT
genomic: GAACTCCCCAGgtacactttc ... tgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcacaagtactttttttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
agttgat putative branch site (score: 5)
ataaaaactagtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacactttcatcattatggtaactatgtcacaagtactttttttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC