Sequence
atgc intronic sequence ATGC exonic sequencegtatttcatattgtctgcactaataattgatgaacttcattaatgaaacactttatattgaaaaggttcactttcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
Basic information
species | Glycine max |
transcript | GLYMA16G05080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatttcatattgtctgcactaataattga-tgaact-tcattaatgaaacactttatattgaaaaggttcactttcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
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--gtctttttttgaattgaaaaatcatcctctgtactatcatt--tgtaattgctcatgtt---aatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
upper sequence: GLYMA16G05080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G26690.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatttcatattgtctgcactaataattgatgaacttcattaatgaaacact-ttatattgaaaagg----ttcactttcttctcttgca-agGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
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gtattttgttttcctt---taaattcttga--aactataatg-caaagtgctattggatagaaatagaatctttacttgtgttatttgtttagGGAGGATGGGAAGATGATGAAACTGTTCTTGAAGCTGCTTCTCGTGAAGCTATGGAAGAAGCAGGAGTTAAAGGAATACTAAGA
upper sequence: GLYMA16G05080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g00870.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtatttcatattg----tctgcactaataattgatgaacttcattaatgaaacactttatattgaaaaggttcactt-tcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
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gtacaattttcctcctctcttcctcccatattggtaattggtatagaaggattgttaccactcttaattaaaattctgaggttttgatttttatcctatgtttgcttgtcagGGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATMapped 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|151406850|gb|EV276665.1|EV276665EST: AAGTACTTATGGTTTCTTCACCAAAACGTGATGACCTTGTATTCCCAAAG GGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCT
genomic: AAGTACTTATGGTTTCTTCACCAAAACGTGATGACCTTGTATTCCCAAAGgtatttcata ... ctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCT
EST:
gi|19054175|gb|BM732842.1|BM732842EST: AAGTACTTATGGTTTCTTCACCAAAACGTGATGACCTTGTATTCCCAAAG GGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCT
genomic: AAGTACTTATGGTTTCTTCACCAAAACGTGATGACCTTGTATTCCCAAAGgtatttcata ... ctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttcattaatgaaacactttatattgaaaaggttcactttcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
cattaat putative branch site (score: 3)
ttcactttcttctctt putative PPT
attaatgaaacacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcatattgtctgcactaataattgatgaacttcattaatgaaacactttatattgaaaaggttcactttcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA