Sequence
atgc intronic sequence ATGC exonic sequence...aatatgtataatgctggaatgcaaaactagatttgtactattggaagaaggagtttgtgaggtcattattattgcctagtgtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
Basic information
species | Glycine max |
transcript | GLYMA04G09780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G019153_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------aatatgtataatgctggaatgcaaaactagatttgtactattggaagaaggagtttgtgaggtcattattattgcctagt--gtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
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gtttgttaactttgcttttgcaattaaattcagttcttcgtttgccattcatcttacacttttgtgaagcaatttttacttttactagaaaatacgcattatgttgaaat-caaggtt---tcaggacaat---agcttggattcttacgaattattatttctttctttttcctgtttctctttgattaaagGAATTGGGTGGACGTCATGGAAGAAAAGATGGTTTATTTTGACACATACTTCGTTGGTTTTCTTTAGAAGCGACCCT
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G24580.1 (Arabidopsis thaliana), 3'ss of exon 3
-aatatgtataatgctggaatgcaaaactagatttgtactattggaagaaggagtttgtgaggtcattattattgcctagtgtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
| | | | || | | ||||| | | | | | ||| ||| | | | | | | |||||| | | ||| ||||| |||||||| ||||||||||| ||||||||||| || | |||||||| |||||||| ||||||| ||
atacaacgacagcactagcacaattcactaggct-acatgtcctggtctgtggctatgtcttaaaattgtctctcaccactttctatttcgtttaatacagGGATTGGCTGGACATCATGGAAGAAAAGATGGTTTATTTTGACGCGTACTTCACTAGTTTTCTTTCGAAGTGACCCG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g07310.t01 (Vitis vinifera), 3'ss of exon 2
-----aatatgtataatgctggaatgcaaaactagatt-tgtactattggaagaaggagtttgtgaggtcattattattgcctagtgtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
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tgaggagtaaatttacttcaaggattctaagattcatcatgtaccattgttgtgaggaattgacta------tatctgaacttgctatttaattcttgttatatagGAATTGGATGGACATCATGGAAGAAAAGGTGGTTTATTTTAACACGTACATCGTTGGTTTTCTTTAGAAGTGATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaggagtttgtgaggtcattattattgcctagtgtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
tcttgac putative branch site (score: 3)
tatttctt CT-rich tract
tcattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatgtataatgctggaatgcaaaactagatttgtactattggaagaaggagtttgtgaggtcattattattgcctagtgtgtatttcttgacttgtagGAATTGGGTGGACATCCTGGAAGAAAAGGTGGTTTATTTTAACACAAACTTCACTTGTTTTCTTCAGAAGTGATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - -aatgctg
- - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - -ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagtgtg