Sequence
atgc intronic sequence ATGC exonic sequencegtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaacaaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
Basic information
species | Glycine max |
transcript | GLYMA01G35690.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G011912_T01 (Zea mays), 3'ss of exon 2
gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaacaaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
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------------------------------------------------------------------ttctgtttgcattcttttggt-agttttccccttggtagttgtgttcata--gtgctgtaatgatttgaag-gtgatctgtgtttattt------tctttgcattg------tcagGGCATGTATAAGCAGCTTCATTTGGAACCATATGCTGTTCATACTACTTTTCAGTATGCGGGCACTGAAGGAAAGCGCCATAGATTGCGAGAGGCAATGC
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaacaaactgtgttcagttttt-cctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
|| || | || || |||| ||| | || | ||| | | | ||||||||| | ||||| | |||| ||| ||| ||||||||||||| |||||||| | || |||||||| ||||| |||||||| || |||||||| || |||||||| |||||| | || ||||| | ||||
----------------------------------------------------------------------gtacctttcttcatgcttc-ctgtttttgtg--ttttattatcatcctcttttctt----------ttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaa--caaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
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-------------------------------------------------------------------------------tctgccatcaa--acttgagaattttgtacctagatcc-atgacatagaacacattaaactttgcattgaacatctttctaag--ccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaacaaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
agttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaacaaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC