Sequence
atgc intronic sequence ATGC exonic sequence...ctagtgggatgaagctattgttttttttgttgcttgtcacatgtacaattatacttgagttttgtcgtgtttaatttattttctgttgatatttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
Basic information
species | Glycine max |
transcript | GLYMA02G46250.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------------------------------------------ctagtgggatgaagctattgttttttttgttgcttgtcacatgtacaattatacttgagttttgtcgtgtttaatttattttctgttgatatttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
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gtacaccatcccgtcccttttctgttccttgtttctctttggttttgatgttccccacctactttttgctgaaagcaaaggactaaaaattgtgttagtggtcttggtttctaaagtagagaatttatattcttttttggtggtta-gtgtatgaa-ataagaaaggttcatcggatcc---ttatttcactttg----ttttccagGTTGATGATACAGAGGTCATTAGCTTCCTTCTTTCAACTGAAATTATTCCTCTGTGCCTCCGTACCATGGAAATGGGGAGTGAGCTGTCAAAAACA
upper sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 7
--ctagtgggatgaagctattgttttttttgttgcttgtcacatgtacaattatacttgagttttgtcg--tgtttaatttattttctgttgatatttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
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attaattgctatattgtttgtattgtttgtaaggtttgttactcttgtgatt----ccaagtattgctggttattaccttttttattttttcccctctttccagGTTGATGATACAGAAGTTATTAGTTTCCTTCTCTCAACAGAAATAATTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACA
upper sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------ctagtgggatgaagctattgttttttttgttgcttg---tcacatgtacaattatactt-gagttttgtcgtgtttaattt------------attttctgttga--------tatttcac---cagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
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gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACCMapped 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|6070480|gb|AW099867.1|AW099867EST: TTGAGTATTTGAGGCTTACCACTCTTGGAGTCATTGGTGCCTTAGTGAAG GTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCG
genomic: TTGAGTATTTGAGGCTTACCACTCTTGGAGTCATTGGTGCCTTAGTGAAGgtacaacctc ... atttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattatacttgagttttgtcgtgtttaatttattttctgttgatatttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
tgttgat putative branch site (score: 4)
tttcacc CT-rich tract
tgtttaatttattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagtgggatgaagctattgttttttttgttgcttgtcacatgtacaattatacttgagttttgtcgtgtttaatttattttctgttgatatttcaccagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
- - - - - - -gctattg
- - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcgtg