Sequence
atgc intronic sequence ATGC exonic sequencegtaacgtattatattctacctcctttcctttttataagaaacaagttatagtgtattatttaaatttaattaacactcattctctcttctcattaaaagaaaagaaaagaaaagaaaagaaaaaccctcactttatgaatattgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGAGGCCTGATTTGAAGAGAGGAATGTTCTCTCAACAAGAGGAGGATCTTAT
Basic information
species | Glycine max |
transcript | GLYMA04G36110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G36110.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 1
gtaacgtattatattctacctcctttcctttttataagaaacaagttatagtgtattatttaaatttaattaacactcattctctcttctcattaaaagaaaagaaaa---gaaaagaaaagaaaaaccctcactttatgaatat-tgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGAGGCCTGATTTGAAGAGAGGAATGTTCTCTCAACAAGAGGAGGATCTTAT
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-------------------------------------------------tgtttat-atcgtaatttagttgctatac-ctctctctttgtatctcactctctgacagtgtgtgaataatataatgtgtgttgctgagttgctgtgtacagGATTGGAGAGGTGTGGCAAGAGTTGCAGGCTGAGATGGATCAACTACCTGAGGCCTGATCTCAAGAGAGGCAGCTTCTCCCAGCAGGAGGAGGAGCTCAT
upper sequence: GLYMA04G36110.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09080.t01 (Vitis vinifera), 3'ss of exon 1
gtaacgtattatattctacctcctttcctttttataagaaacaagttatagtgtattatttaaatttaattaacactcattctctcttctcattaaaagaaaagaaaagaaaagaaaagaaaaaccctcactttatgaatattgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGAGGCCTGATTTGAAGAGAGGAATGTTCTCTCAACAAGAGGAGGATCTTAT
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-----------------------------------------------gtaattaatttctcttcttcaccttccacattttcatctttcttggtagttg-------------------gtaaattgttttgatggtgatctttgtagGTTTGCAGAGGTGCGGAAAGAGTTGCAGATTGAGATGGATTAACTATTTGAGACCCGACCTTAAGAGAGGAATGTTCTCTCAGCAAGAGGAGGATATCATMapped 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|151401352|gb|EV271166.1|EV271166EST: CATAACCAGATTTGGCGTTGGCTGCTGGAGCTCCGTTCCCAAACAAGCCG GACTCCAAAGGAGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGA
genomic: CATAACCAGATTTGGCGTTGGCTGCTGGAGCTCCGTTCCCAAACAAGCCGgtaacgtatt ... aatattgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaagaaaagaaaagaaaagaaaagaaaaaccctcactttatgaatattgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGAGGCCTGATTTGAAGAGAGGAATGTTCTCTCAACAAGAGGAGGATCTTAT
ccctcac putative branch site (score: 3)
aaaagaaaagaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgtattatattctacctcctttcctttttataagaaacaagttatagtgtattatttaaatttaattaacactcattctctcttctcattaaaagaaaagaaaagaaaagaaaagaaaaaccctcactttatgaatattgcagGACTCCAAAGGTGTGGAAAGAGTTGCAGATTGAGATGGATAAACTATTTGAGGCCTGATTTGAAGAGAGGAATGTTCTCTCAACAAGAGGAGGATCTTAT
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