Sequence
atgc intronic sequence ATGC exonic sequence...atatcttacgtttatagatcatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttgtattatattttagtttttaatgtgacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
Basic information
species | Glycine max |
transcript | GLYMA14G03520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 4
atatcttacgtttatagatcatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttg--tattatattttagtttttaatgt-----gacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
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gtactgaataac-attcattatc-tacagtgaactttttcttttttatgctggaattgttttaaattgtttaactgacatatttgtgtcctggctgtatgctgacagGTTTCTGTGGGCTACTTCATCGCTGACCTTGCAATGATCTTCTGGTTGTATCCTTCCCTTGGTGGAATGGAATAC
upper sequence: GLYMA14G03520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 5
--atatcttacgtttatagatcatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttgtattatattt--tagtttttaatgtgac-agGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
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aactttcttgggactaaaggctttgttgtttt----ttcaagaaaaaaaaggctttgtc-agtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
upper sequence: GLYMA14G03520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 3
-atatcttacgtttatagatcatcatattatgagctgcaacacatttttgttttta-tctggtcatgaaatttgtattatattttagtttttaatgtgacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
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aatggctaacaaccttc--tccttgtggcagtgtttacattacctcctgttatccaatctgagaagcaagtatatgtttcatattttgatgtgttttgacagGTTTCTGTTGGTTACTTCCTTGCTGATCTTGGGATGATATGTTGGTTTTATCCATCCCTAGGCGGAATGGAGTATMapped 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|308098376|gb|HO760117.1|HO760117EST: CCGAACTTATTACATTTCGAAGCTCTTCATCATCTACCTTTGCTCTGGGG GTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTT
genomic: CCGAACTTATTACATTTCGAAGCTCTTCATCATCTACCTTTGCTCTGGGGgtaagaatga ... aatgtgacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtttttatctggtcatgaaatttgtattatattttagtttttaatgtgacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
ttttaat putative branch site (score: 3)
tcatgaaatttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatcttacgtttatagatcatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttgtattatattttagtttttaatgtgacagGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA