Sequence
atgc intronic sequence ATGC exonic sequence...tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
Basic information
species | Glycine max |
transcript | GLYMA02G46530.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
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---------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatc----acacaatactcatctgaaaact-ttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
upper sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
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--------------gtgggtggttt--ctcccctttcctgctctaact-tatctgcaaattgttatcatgtaccttatgagtgaacat-------tgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
upper sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
-----tcacttcttcata-attgggcattttggctttgc--attcatg-tcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
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gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtata---tattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
upper sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttc---ttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
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--actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatc-ctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACCMapped 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|16284343|gb|BI946034.1|BI946034EST: CAGATGACGTTCTACGGCAAGGAGTACAGGGAATATCAGACATTATAACT GTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAA
genomic: CAGATGACGTTCTACGGCAAGGAGTACAGGGAATATCAGACATTATAACTgtgagttgat ... cttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAA
EST:
gi|16277659|gb|BI942496.1|BI942496EST: CAGATGACGTTCTACGGCAAGGAGTACAGGGAATATCAGACATTATAACT GTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAA
genomic: CAGATGACGTTCTACGGCAAGGAGTACAGGGAATATCAGACATTATAACTgtgagttgat ... cttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
tgccttctt CT-rich tract
tttttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- -cttcttc
- - - - - - - - -ggcattt
- - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - tgtcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg