Sequence
atgc intronic sequence ATGC exonic sequence...aatcagcttcttatgcatttacttcatatattttggaatccgagatcttgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
Basic information
species | Glycine max |
transcript | GLYMA03G29860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g10130.1 (Oryza sativa), 3'ss of exon 3
----aatcagcttcttatgcatttacttcatatattttggaatccgagatcttgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
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tctgtgttgtattgtgacgtagctgctttgtgtattt--aattttgtgatcatggaggtgg-gactccacatttttggtt-ttcttaacaaacagcttttgtagGTTTTAAATTGCCATGAGTCTGTTATCTACATATTGGCACCATTGAAGTACGCAACTGTGTATGGATGTTCTGATGCTACTGTTGTTCTTGGTGCTATTG
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 3
aatcagcttcttatgcatttacttcatatattttggaatccgagatct---tgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
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tatc-gcttcatgactaatgacttga-acaatgaaacctcaaaggtaggagtaggactatgcttgctttatctatgacc-taaattgcaaacttcttttgtagGTTTTGAACTGTCATGATTCTGTTATCTACATATTAGCACCACTGAAGTATGCTACTGTGTATGGTTGTTCTGATGCTACGGTTGTTCTTGGTGCTGTTG
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 3
aatcagcttcttatgcatttacttcata----tattttggaatc--cgagatc--ttgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
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-------ctcacatgcatcgagcaaacaagcacaatctgaaatttgcgtgttccattgtataatttgt-gtttttggcttacttcaacatagtgttgtacaattgcagGTTCTGAATTGCCATGATTCTGTCATTTACATTTTAGCGCCATTGAGATTTGCCACCATCTATGGATGCTCTGATGCAACTATAGTTCTTGGAGCAGTTGMapped 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|254316387|gb|GR827924.1|GR827924EST: AATCGTCATATGCTAAGCATGCATCTGACATTAAAGGTTCCTCCGTTAAG GTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATAT
genomic: AATCGTCATATGCTAAGCATGCATCTGACATTAAAGGTTCCTCCGTTAAGgtttgtctta ... gtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
tattaat putative branch site (score: 2)
ttattaattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcagcttcttatgcatttacttcatatattttggaatccgagatcttgaaacttttgtcactataggcatgcttattaattatgtttggtcattgcagGTTCTAAATTGCCACGAGTCTGCCATCTACATCTTAGCACCATTGAGATATGCTACTGTCTATGGATGTTCAGATGCAACAATAGTTCTAGGAGCAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- -cagcttc
- - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg