Sequence
atgc intronic sequence ATGC exonic sequencegtaaggacacttctctttctttttcccactcatgcctttggtgttttcatttccctcttttatgtcatggccttttgcatttctcttcatgaacagttaaaaaaaaaattcatacttgcacccttctaattttgtggtccctctctctctttttctttctctgtgtttgttgtttttcagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
Basic information
species | Glycine max |
transcript | GLYMA09G29810.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126646_T01 (Zea mays), 3'ss of exon 1
gtaaggacacttctctttctttttcccactcatgcctttggtgttttcatttccctcttttatgtcatggccttttgcatttctc-ttcatgaacagtta-aaaaaaaaattcatacttg-cacccttctaattttgtggtc-cctctctctctttttctttctctgtgtttgt-tgttttt-cagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
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---------------------------gtacgtgccgatt-tacccccctctccctctctc----cattatctactgcgtgcctggttagtggttagccgtacgtgtttgttcgttttggatgctttgctcaaatggcggcggcggcggcggcgtttgccttgtctgtgcttgtgcgcgcccgcagGATGTTCAAGGAGTGCCCGCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAAC
upper sequence: GLYMA09G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G145690_T02 (Zea mays), 3'ss of exon 1
gtaaggacacttctctttctttttcccactcatgcctttggtgttttcatttccctcttttatgtcatggccttttgcatttctcttcatgaacagttaaaaaaaaaattcatacttgcacccttctaattttgtggtccctctctctctttt-tctttctctgtgtttgttgtttttcagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
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--------gtacgtgcaccctgctggccggcaggcctgcgccgatttc---cccctcccttccgtccttatctactgg--ctggtttggttagctagctgtacgtgtttgctcgttttggctgctctgctcaaatggcggcggcgtctgtcttgtctgtgcctgtgcgcgcc----cgcagGATGTTCAAGGAGTGCCCGCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAAC
upper sequence: GLYMA09G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0053g00780.t01 (Vitis vinifera), 3'ss of exon 1
gtaaggacacttctctttctttttcccactcatgcctttggtgttttcatttccctcttttatgtcatggccttttgcatttctcttcatgaacagttaaaaaaaaaattcatacttgcacccttctaattttgtggtccctctctctctttttctttctctgtgt--ttgttgtttttcagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
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---------------------------------------------------------------------------------------------------gtaagattgatgagagttgaaatttcttatttgtttgtttgttggtttggcaaatagtttgaaatataatattggtaatgaagGATGTTCAAGGAGTGTCCTCACCCAGATGAGAAGCAGAGGCTGCAGTTGAGCAGAGAGTTGGCTTTGGCTCCCAGGCAGATCAAATTTTGGTTTCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaattttgtggtccctctctctctttttctttctctgtgtttgttgtttttcagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
ttctaat putative branch site (score: 2)
tccctctctctctttt putative PPT
tttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggacacttctctttctttttcccactcatgcctttggtgttttcatttccctcttttatgtcatggccttttgcatttctcttcatgaacagttaaaaaaaaaattcatacttgcacccttctaattttgtggtccctctctctctttttctttctctgtgtttgttgtttttcagTATGTTCAAGGAGTGTCCGCACCCAGATGAGAAGCAGAGGTTGCAGTTGAGTAGGGAGTTAGGCTTGGCGCCTAGACAGATCAAATTTTGGTTCCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA