Sequence
atgc intronic sequence ATGC exonic sequencegtagatgctggtgccttgctgtttttttttatttaattatattttataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
Basic information
species | Glycine max |
transcript | GLYMA05G04150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 3'ss of exon 3
gtagatgctggtgccttgctgtttttttttatttaattatattttataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
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--gtatgtta-----tcatcagttactgtgaatggctcatattctggtattagaaccttgtgttgag--tatcgaccgctctgaaaatttta-------gGTTAGAGTTCCTGTTGGAAAATTTATATTGGAACTACCTGCTGGGATGCTAGACGATGAAAAGGGAGATTTTGTTGGCACTGCAGTCCGTGAG
upper sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G337631_T01 (Zea mays), 3'ss of exon 5
gtagatgctggtgccttgctgtttttttttatt-taatt-atattttataactggattttcatgttatggctattgttatgttggatattcttatttgta-agGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
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-atgatgtgcttaccaaacaggtatagtgtaccatgattgagagcacatgaattgatattcagtaaacaa--attcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTCCCTGCTGGGATGCTAGATGATGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG
upper sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 3
gtagatgctggtgccttgctgtttttttttatttaatt-atattttataactggattttcatgttatggctattgttatgttggatattcttatttgta-agGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
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--------------------gtatagtgtaccatgattgagagcacatgaattgatattcag--taagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG
upper sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagatgctggtgccttgctgtttttttttatttaattatattt-tataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
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--------------------------gtatctctatttatgttcgtgttgttctattttttaacaaagatcaacattatacgggttgtt-----ttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
upper sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g04840.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------gtagatg-ctggtgccttgctgtttttttttatttaattatattttataactggattttcatgttatggctattgttatgttggatattct--------------tatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
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gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAGMapped 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|192321665|gb|FK014009.1|FK014009EST: TGATGCTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG GCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTG
genomic: TGATGCTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAGgtagatgctg ... tatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
ttataac putative branch site (score: 2)
ttcttattt putative PPT
atattcttatttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatgctggtgccttgctgtttttttttatttaattatattttataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG