Sequence
atgc intronic sequence ATGC exonic sequencegtaatgctgaactgctaatcatcaatgtttatttcaatagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
Basic information
species | Glycine max |
transcript | GLYMA07G39240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g44130.1 (Oryza sativa), 3'ss of exon 3
gtaatgctgaactgctaatcatcaatgtttatttca-atagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
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----------gttctt--ttatcattttcgaaattatatgcttaatctgacagaacact----atgaactgtcaatgctca--tgttactgaactgaattatgttc-ccagGAATTCATTGAAGCTACTCATGAGCCTGGTCTTACGTTTCTAGCAGCAAAATTTGATGGCATCCTTGGACTTGGATTTAAGGAAATTTCAGTTGAAGGTG
upper sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgctgaactgctaatcatcaatgtttatttcaatagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgata--cccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
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--------------------------gtaaactatatgtccgaccctaatcag--tactcttacaacatacacatcaatgacctccttcttaacatttgtctatctcatcagGAGTTTATCGAGGCAACCAAGGAGCCTGGTATAACATTTGTTGTAGCTAAATTTGATGGTATCCTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAG
upper sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgctgaactgctaatcatcaatgtttatttcaatagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
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--------------gtgattttgagcagtttttcctcttgaatttg---attgattattttgactatg-gctgccta-----tgctaaaa--actgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGMapped 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|193361480|gb|FK327342.1|FK327342EST: TGTAAAGAACCAG GAATTTTATTTGAAGCGACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCA
genomic: TGTAAAGAACCAGgtaatgctga ... tacccatcagGAA-TTTA-TTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCA
EST:
gi|193350645|gb|FK316319.1|FK316319EST: TCTTTAGCTACGACAGTGTCAGAGTTGGTGATATATTTGTAAAGAACCAG GAATTTATTGAAGCAAC
genomic: TCTTTAGCTACGACAGTGTCAGAGTTGGTGATATATTTGTAAAGAACCAGgtaatgctga ... tacccatcagGAATTTATTGAAGCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
ttttgat putative branch site (score: 4)
ataatatgttgattag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgctgaactgctaatcatcaatgtttatttcaatagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA