Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctcttgtactatgcatttagtgctaggctcacccccctccccccaattttcgttcgtcttgaattctgattctgtctagaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
Basic information
species | Glycine max |
transcript | GLYMA02G31320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
gtaag--tctcttgtactatgcatttagtgctag-gctcacccccct-ccccccaattttcgttcgtcttgaattctgattctgtctaga--attttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
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gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G037104_T01 (Zea mays), 3'ss of exon 3
gtaagtctcttgt-actatgcatttagtgctaggctcacccccctccccccaattttcgttcg---tcttgaattctgattctgtctaga--attttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
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gtaaggagcccatcattaatagtttcattgtttgcat-tcaccttcatgcaagtttaaggacaaaagtttggcttacaagcttatctaaataattccacagGTAAAGAGCATGCACTCATCATATCAAATCATCGGAGTGATATTGATTGGCTCATTGGATGGATATTGGCCCAG
upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtctcttgtactat--gcatttagtgctaggctcacccccctccc---cccaattttcgttcgt---------cttgaattctgatt--ctgtc----tagaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
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gtaagttcatatgcttattggcaatcaa-atcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtctcttg--tactatgcatttagtgctaggctcacccccctccccccaa-----ttttcgttcg---tcttgaattctgattc--tgtcta--------gaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
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gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAGMapped 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|19348278|gb|BM892810.1|BM892810EST: GTCCAAGTATTCACAGATCCTGAAACCTTTCATTCAATGG GTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGC
genomic: GTCCAAGTATTCACAGATCCTGAAACCTTTCATTCAATGGgtaagtctct ... aattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGC
EST:
gi|13791554|gb|BG654145.1|BG654145EST: GTCCAAGTATTCACAGATCCTGAAACCTTTCATTCAATGG GTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGC
genomic: GTCCAAGTATTCACAGATCCTGAAACCTTTCATTCAATGGgtaagtctct ... aattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctccccccaattttcgttcgtcttgaattctgattctgtctagaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
ttctgat putative branch site (score: 3)
ttttcc putative PPT
tagaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctcttgtactatgcatttagtgctaggctcacccccctccccccaattttcgttcgtcttgaattctgattctgtctagaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA