Sequence
atgc intronic sequence ATGC exonic sequence...gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
Basic information
species | Glycine max |
transcript | GLYMA12G06690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-----------------------gtaagttttgcaccttcccttg-tgagcaat-gcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-------------gtaagttttctgcttcccttcccttgcac--accattctat-gccatat---catggttgcc--tgaactgttaatccatttttcagCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-------gtgagttttctccttcccttgccttgc-acaccgttcggtgccatat---catg---gttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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gtaagtattagtatttacacacaaaaaactcgtatt---gacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtga-atttttat-atagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtacttta-tgtaatca-tcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-------------------gtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------gcttgttgttggagttcttgtt--cttcaatcttcctgttgcattgaataaactatag-gcatgtgtattta--------ttcactgttgtact--ttatgtaatcatc---acagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggctgttttatttcatcatttttcgtgtaagtgcagttcataagcacttcgctggagtaataatgaggttcttgtttgtgcagGCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG-----------------Mapped 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|193682919|gb|FK625067.1|FK625067EST: AGATCAAGCAGATGAATCAGAGGATCCATACATGCGGTTAGTTTATGCAA CATCATGGGCTATATCGGTGTACTTT
genomic: AGATCAAGCAGATGAATCAGAGGATCCATACATGCGGTTAGTTTATGCAAgtgagtaatt ... atcatcacagCATCATGGGCTATATCGGTGTACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
tgtatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - gttgttg
- - - - - - -gttcttg
- - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - -gaataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg