Sequence
atgc intronic sequence ATGC exonic sequence...gaacttgctggctacttaaactagattgaaaatttagacacatgtaacatcctattcctatgtattttatgtaatgtttagtttctaccttcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
Basic information
species | Glycine max |
transcript | GLYMA13G31880.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31880.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30040.1 (Oryza sativa), 3'ss of exon 2
gaacttgct--ggctacttaaactagattgaaaatttagacacatgtaacatcctattcctatgtattttatgtaatgtttagtttctaccttcttt-tgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
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---gttgctaagattctctctgccgatctgatccatttgactggtgaaatgcaaaatcagcaagaatgtctgattgctcttgttttttttttcattcgttcagGAGAAAAACTGGGAATGTGGCTATCTCTTTTCCCAACTATTTATCTGTCGGCAGGCAGTGCAACTGCGTTGATCCTTGTTGGAGGGGAGACCATGAAGCT
upper sequence: GLYMA13G31880.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G125832_T01 (Zea mays), 3'ss of exon 2
gaacttgctggctacttaaactagattgaaaatttagacacatgtaac---atcctattcctatgtattttatgtaatgtttagtttctaccttcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
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gtggcttttgtctatttcatcgatagctacacctacaagtcacatgacggaaaaggatttccaccaatt--atatactcacaaatatatattgttcatc-cagGAGAAAAAATGGGAATGTGGCTGGCTCTTTTCCCAACTATTTATCTCTCGGCAGGCACTGCAACTGCACTGATCCTTGTTGGAGGGGAGACCATGAAGCT
upper sequence: GLYMA13G31880.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G47670.1 (Arabidopsis thaliana), 3'ss of exon 2
----------gaacttgctggctacttaaactagattgaaaatttagacacatgtaaca--tcctattcctatgtattttatgtaatgtttagtttctacc-----------ttcttttg-------cagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
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gtaaaatgataaatttagttttacattaagaatgatgaaataatgcatcaatagtgacaattattattgatactaattttgtgtcttgctaagttgctattactaaatcttgtactcttgattggaacagGAGAAAGGTTAGGAGTATGGCTTGCATTGTTTCCTACGGTTTACTTATCAGCAGGAACCGCGACAGCGCTGATTCTGATCGGTGGAGAGACAATGAAACT
upper sequence: GLYMA13G31880.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g11300.t01 (Vitis vinifera), 3'ss of exon 2
gaacttgctggctacttaaactagattgaaaatttagacacatgtaacatcctatt---cctatgtattttatgtaatgtttagtttctaccttcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
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-acatagctgatgcttttgatttaggggaca--taggactcgaggaaggtcttttaagattttggcttctgatctaatactttatttatttatttattttcagGAGAAAGACTGGGCGTTTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTCTGATTCTCATAGGAGGGGAAACCATGAAACTMapped 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|192325203|gb|FK017559.1|FK017559EST: TCCAGGTAAAAGATACAACAGATATGTGGAGCTAGCACAAGCAGCATTTG GGGAAAGATTATGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAG
genomic: TCCAGGTAAAAGATACAACAGATATGTGGAGCTAGCACAAGCAGCATTTGgtaagcttgt ... tcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAG
EST:
gi|208303202|gb|GE101471.1|GE101471EST: TCCAGGTAAAAGATACAACAGATATGTGGAGCTAGCACAAGCAGCATTTG GGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAG
genomic: TCCAGGTAAAAGATACAACAGATATGTGGAGCTAGCACAAGCAGCATTTGgtaagcttgt ... tcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatcctattcctatgtattttatgtaatgtttagtttctaccttcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
atgtaac putative branch site (score: 3)
tttctaccttcttttg putative PPT
tatgtattttatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaacttgctggctacttaaactagattgaaaatttagacacatgtaacatcctattcctatgtattttatgtaatgtttagtttctaccttcttttgcagGGGAAAGATTAGGAGTCTGGCTTGCTCTCTTCCCAACTGTTTATTTGTCAGCAGGAACTGCAACAGCTTTGATTCTTATTGGAGGAGAGACCATGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - -tgctggc
- - - - - - - - - - - - - - - - - - - - catgtaa