Sequence
atgc intronic sequence ATGC exonic sequencegtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
Basic information
species | Glycine max |
transcript | GLYMA16G00400.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 8
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
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------------------------gtctggcatgttcagtttc--cctccctctggttcttacctttttgcttcttctgatatcattca--tccat--gtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttc--tttgttttctgtctt-ctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
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---gttaaagcatgatttt--tgcattagctatatgttgttctattcattcagtttattccttgtcttactattttgtgcccttg----ctaatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttct-gtcttctttttca--ttttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
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----gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaacc-atcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtatttggtgcaa-gaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
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gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgctt---ttgatg--ggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAGMapped 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|26047783|gb|CA784461.1|CA784461EST: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG CCCTTGTTTCCTGGAGAGAGTGGAGTT
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtg ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
agttgat putative branch site (score: 5)
ttctttttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT