Sequence
atgc intronic sequence ATGC exonic sequence...agcaacatcaatctcttgtatagtatccactttttcggatagaagttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
Basic information
species | Glycine max |
transcript | GLYMA05G29870.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------------------------------------------------------------------agcaacatca----atctcttgtatagtatccactttttcggatagaagttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
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gtatgcctcaccttttgtttatcgagttgtaaccacattggaatacataattgtgcagatgactaatagaattaataaatgatgaagcgacttcccttgcgatacccctgtaattttagtcttaagtttgttgcttctagtcctaatatt-aatgctacaccaactgtttggtgctgtcctaatttggtagtaaattgcagGTATCTACATTTGCTGATATGGAAGGTGAAGAGACATTCGATTCATCGTTCCTTGGACATGCTGATGAAGTTGTTGAGGAAAGAATTGCTGATGATGATG
upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
agcaacatcaatctcttgtatagtatccactttttcggataga---agttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
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-gaaatgtcaaaacgtcttataat-ttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaaccttt-cagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 11
agcaacatcaatctcttgtatagtatccactttttcggatagaagttttgaatact-atttcctttatgtatcattggacttgat----ttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
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--------------------------gtacttcctgcgctaggctttttcaatacccatgttgtcaaactaaaatttcaactaatatatttatcctttattttagGTCACCACTTTTGCTGACATGGAGGGCGAAGAAACATTTGATCCAGCTCACCTTGGATCTGCTGATGAGGTTGTTGAAGAGAGAATCGCAGATGATGATG
upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 11
agcaacatcaatctcttgtatagtatccactt-tttcggatagaagttttgaatact--atttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
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--catggatattatgttatgctacttgtgcttatcttttatgatagtcaaagatacccaacttatcttgtttatcgttatg-ttacccttcgatgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTTCTTGGATATGCAGATGAAGTTGTGGAGGAACGCATTGCAGATGATGATGMapped 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|26045589|gb|CA783128.1|CA783128EST: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggctttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST:
gi|24136371|gb|BU926881.1|BU926881EST: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggctttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
ctttgac putative branch site (score: 4)
tttttacttt CT-rich tract
ttgatttttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcaacatcaatctcttgtatagtatccactttttcggatagaagttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- caacatc