Sequence
atgc intronic sequence ATGC exonic sequence...atacttgcatttttaaggataaatctggaaaatcatatttgtatcttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
Basic information
species | Glycine max |
transcript | GLYMA20G02130.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38490.1 (Oryza sativa), 3'ss of exon 2
atacttgcat-ttttaaggataaat-ctggaaaatcatatttgtatcttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
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caacttccatgccatgtgggtgggtgccttttttacacaatcgaatgctga-cagtatttcaggttaccacc-ttacaatcttttttttacttttttattagGTCTGCCTGAATCAAATGGATACATATATATTGAGGCAAATGGTGGTTTGAATCAACAAAGGACATCG
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G382792_T02 (Zea mays), 3'ss of exon 2
----atacttgcatt---tttaaggataaatctggaaaatcatatttgtatcttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
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ttcgtgactggaattagttccatacttccatttagaaaact---tgcatatctattcctcctaatttatctctgt---ctaataatttat-tccatacttctgttagGTTTACCTGAATCAAATGGCTACATATACGTTGAGGCAAATGGTGGTTTAAATCAACAAAGGACATCA
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 2
lower sequence: AC213621.5_FGT002 (Zea mays), 3'ss of exon 3
-atacttgcatttttaaggataaatctggaaaat---catatttgtatcttctt-cagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
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tgtgaccggaatt----agttctgtttagaaaacttccatatttatttcccctgacctctctctctctctctctctctactaatgtat-tccatacttctgttagGTTTACCTGAATCAAATGGCTACATATACGTTGAGGCAAATGGCGGTTTAAATCAACAAAGGACATCG
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G01480.1 (Arabidopsis thaliana), 3'ss of exon 2
atacttgcatttttaaggataaatctggaaaatcatattt-gtatcttcttcagtgtactga-gttttgttaactatgaatttatatttcttt-tgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
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---tgtacgttctgcaaagttttgcctggagctcagatttagtctgttgtttggagcataattgattaattgggtatctgcttttttttgtttataattgtagACTTGCCTGAGTCAAACGGTTACATATATGTTGAGGCAAATGGAGGCTTGAATCAGCAGCGGACATCG
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g05000.t01 (Vitis vinifera), 3'ss of exon 2
---atacttgcatttttaaggataaatctggaaaatcatatttgtatcttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
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ctaaccctttcttgtttttgca-aaatcttagtagtattatgcgcacaaatgtccttcaatagctattattttaacatgaggttgttgtttatccat--gtagGCTTACCCGAATCAAATGGTTACATATATGTTGAGGCAAATGGTGGCTTGAATCAGCAGAGAACATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
tgttaac putative branch site (score: 2)
tttatatttctttt putative PPT
ttttgttaactatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atacttgcatttttaaggataaatctggaaaatcatatttgtatcttcttcagtgtactgagttttgttaactatgaatttatatttcttttgttgatagGCCTACCCGAATCAAATGGATACATATATGTGGAGGCTAACGGTGGCTTAAATCAGCAGAGGACATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA