Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgttgccagtgactggtttattaaggttgagacaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
Basic information
species | Glycine max |
transcript | GLYMA19G27480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
ttgttgttgccagtgactggttt--attaaggttgagacaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCC-ACCTG
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ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatc--tcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
upper sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g32100.1 (Oryza sativa), 3'ss of exon 1
ttgttgttgccagtgactggtttattaagg----ttgagacaattcctttatgtat-taggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
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--ggtactactaatatcattcatatgaaagcaattctatagtgatgcattatacttgtgatgatttagcaataagatgattatatgtgtttgca---attggtagATGGACAGGGCTTCCATTCTCGGCGACGCGATTGAGTACCTGAAGGAGCTGCTGCAGAAGATCAATGATCTTCAGAATGAGCTCGAGTCGTCCCCCGCGA
upper sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------ttgttgttgc-cagtgactggtttatt----aaggttg-agacaattcctttatgtattaggagcttagga--atggt-gcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
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gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
upper sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 3'ss of exon 1
ttgttgttgccagtgactggtttattaaggttgag----acaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
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atggaccgatcatagactgataatccattgttctgttgcataattggatggtttgggaagatatttaggattacctgtttaaatgttcttt----tgttgatagATGGATAGAGCTTCAATCCTGGCGGATGCTATTGAGTACTTGAAGGAGTTACTGCAGAGGATCAACGACCTCCAGAATGAACTGGAGTCTATCACACCTCMapped 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|298178876|gb|HO024611.1|HO024611EST: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAG ATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
genomic: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaa ... ttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
EST:
gi|23730171|gb|BU763190.1|BU763190EST: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAG ATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
genomic: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaa ... ttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
tactaat putative branch site (score: 1)
ttctttcatttgtt CT-rich tract
atactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgttgccagtgactggtttattaaggttgagacaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - tgttgcc
- - - - - - gtgactg
- - - - - - - - - - - - - - ggttgag
- - - - - - - - - - - - - - - - - - caattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatact