Sequence
atgc intronic sequence ATGC exonic sequence...gaagtttcactttgatgtattttatgttttcaaacctgttcctcttatcttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
Basic information
species | Glycine max |
transcript | GLYMA13G23850.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 5
----gaagtttcactttgatgtattttatgttttcaaacctgttcc---tcttatcttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
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gtaagtaggcacagttctttcttttttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 5
----------gaagtttcactttgatgtattttatgttttcaaacctgttcctcttat-cttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
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gtgagtataagcagcctttctcttaaccctttgatttcgtcatcgcttctatttttattcagctgtatttgaataagcccgttcttacatcatacgggatcgatttt-cagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA
upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 5
gaagtttcactttgatgtattttatgttttcaaacct----gttcctcttatcttctcaa-ggtggaaaaactttctcatttgttggcaataatctgt---tggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
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-------ctctttgatatatttttggtcaaaagacttcataatctgtcctaaaatctcgatgattgctttgatctgtcaaggcttgata-taattggtgtttgaacagGAGCTTGGTCTGTACAAGGCTCAAACAAAGCTTCCATTTAATGCATTTGGAACAATGGCCATGGCAAGAGATMapped 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|31474483|gb|CD416511.1|CD416511EST: AAATTACGGTGAATGGAGAAAAGGCACCTGTTTATGGATCAACTTTAGAG GAGCTTGGTCTATACAAGGCTCAAACGAAGCTTCCCTTTAATGCTTTCGGT
genomic: AAATTACGGTGAATGGAGAAAAGGCACCTGTTTATGGATCAACTTTAGAGgtaatcttca ... tgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGT
EST:
gi|209701690|gb|BW673137.1|BW673137EST: ATCAACTTTAGAG GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGT
genomic: ATCAACTTTAGAGgtaatcttca ... tgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
aaaaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagtttcactttgatgtattttatgttttcaaacctgttcctcttatcttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - tgatgta
- - - - - - - - - - - - - - -tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggc