Sequence
atgc intronic sequence ATGC exonic sequence...ctgtcataattgaaagtcctcatggtcttttattttggtaatcttcaactccttcaacttggtgatcctcttacagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA
Basic information
species | Glycine max |
transcript | GLYMA12G30990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
--------------ctgtcataattgaaagtcctcatggtcttttattttggtaatctt-caactccttcaacttg-gtgatcctcttacag--------attttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA---
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gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.3 (Oryza sativa), 3'ss of exon 2
ctgtcataattgaaagtcctcatggtcttt-tattttggtaa--tcttcaactccttcaacttggtgatcctcttacagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA---
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acatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.5 (Oryza sativa), 3'ss of exon 3
ctgtcataattgaaagtcctcatggtcttttattttggtaa--tcttcaactccttcaacttggtgatcctcttacagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA---
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-tcttgcttctgtcttctttctttgtctac-atttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
ctgtcataattgaaagtcctcatggtcttttattttggtaatcttca---actccttcaacttgg-tgatcctcttacagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA
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--aaggggattaggttcctctcccttttgatattttgaaaatcttgggggagtcttttattttgcctgatactc--agagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGAMapped 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|209719800|gb|BW674952.1|BW674952EST: AGCAATTGTTCTGCATGGAGTTAAGGGTAGAAATGATGAGGGCAAAGCAT CTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGC
genomic: AGCAATTGTTCTGCATGGAGTTAAGGGTAGAAATGATGAGGGCAAAGCATgtatgtttcc ... attcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactccttcaacttggtgatcctcttacagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA
ctcttac putative branch site (score: 3)
ttcttgc putative PPT
agatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtcataattgaaagtcctcatggtcttttattttggtaatcttcaactccttcaacttggtgatcctcttacagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA
- - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg