Sequence
atgc intronic sequence ATGC exonic sequencegtatgtagcatttagttcatgtgttatttgtacagaggtctacaaaaaagactggctttgtcatgctcataatgcatggtggaattagtttagctcattcaaagcatgtgtactcaaatttctttttagttgtttgttttaaataatttcaatttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
Basic information
species | Glycine max |
transcript | GLYMA02G09820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09820.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 6
gtatgtagcatttagttcatgtgttatttgtacagaggtctacaaaaaagactggctttgtcatgctcataatgcatggtggaattagtttagctcattcaaagcatgtgtactcaaatttctttttagttgtttgttttaaataatttcaatttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
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------------------------------------------tgaataccacttccattgttacatgaaaaac-tgtgaagtaatttgtaca-ctgattttctaaatccatgactagattattttaca-----------caaataatgct--------tccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
upper sequence: GLYMA02G09820.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 3'ss of exon 4
--------------gtat-gtagcattt----agttcatgtgttatttgtacagaggtctacaaaaaagactggctt--tgtcatgctcataatgcatggtggaattagtttagctcattcaaagcatgtgtactcaaatttctttttagttgtttgttttaaata-atttcaattta-tgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
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gtaaggagcactgcttatcgttacatctctatgattaatg-gacatttatttaatgctggatagaaaggagtactttattggaaaagtttaaacagatttataattaagtttaacacatataatgtttgctgagtca---ttcaaattgtgtcttggctttgaggagattttggttcaatatgcagGGTCTTTCTCTGGCCTGGGGTTTCTATCATTGTACTTATCTGGAAAAATACGAGCATTTGACAATAGAGGCCATGTTGCAAAACTTTGCATTGTGTTTCTMapped 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|58016374|gb|CX703116.1|CX703116EST: AAAGGTCATAAAGGAAGGATATAAGAGTTTCCCAAGCGGCCATACTTCAT GGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAA
genomic: AAAGGTCATAAAGGAAGGATATAAGAGTTTCCCAAGCGGCCATACTTCATgtatgtagca ... ttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAA
EST:
gi|58019486|gb|CX706228.1|CX706228EST: A-GTCATAAAAGGAAGGATAT-AGAGTTTTCCCAAGCGGCCATACTTCAT GGTCTTTTGCTGGTCTGGGTTTTTTATCATNGTACTTATCTGGAAAAATAA
genomic: AGGTCAT-AAAGGAAGGATATAAGAG-TTTCCCAAGCGGCCATACTTCATgtatgtagca ... ttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtactcaaatttctttttagttgtttgttttaaataatttcaatttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
aaatttctttttagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtagcatttagttcatgtgttatttgtacagaggtctacaaaaaagactggctttgtcatgctcataatgcatggtggaattagtttagctcattcaaagcatgtgtactcaaatttctttttagttgtttgttttaaataatttcaatttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG