Sequence
atgc intronic sequence ATGC exonic sequence...tttcatgtttcttttttttttaacaagggatccaaattttgacagtggaacaagttatacagtaaacattaatacggatcatgtgatatgactattgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
Basic information
species | Glycine max |
transcript | GLYMA11G35080.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g00330.t01 (Vitis vinifera), 3'ss of exon 6
tttcatgtttctttttttttta-acaagggatccaaatt-ttgacagtgg--aacaagttatacagtaaacattaatacggatcatgtgatatgactattgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
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--agattttacacactattgcagacaggttattccaattattagcatttctcaacaaactaattgg--ggttctgggttttctttcgttttttttttcttctagGGAAATCATGCATGCAATGTGGAAGCCTCAAAAATTCAAGTACATATACCTTGTTGCCACCCTATATGTATTCACCCTAACAATTCCATCGGCTGTTGCG
upper sequence: GLYMA11G35080.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 5
---------------------------------------------------------------------------tttcatgtttcttttttttttaacaagggatccaaattttgacagtggaacaagttatacagtaaacattaatacg-gatcatgtgatatgacta-----------------ttgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
|||| |||| | | | | ||| || | | || | |||||| | || || | | || || |||||| |||| |||||| |||||||||||||| |||||||||||| ||||| || | | || || | |||| | |||||| ||||| | || |||||||||||| |||
gtaagtcgatcatgattctcacggcaccactttgcttgatcctacgatatcattccatcgattccctcctttttctttcctgttcttcctgctcagatcaaatcatacccctccggat--caaatcaagttttttcttacttctttttgcaagaccagatgatataactaagttgtttgtggttttcttgcagAGAAATCATGCATGCTATGTGGAAGCCTTCAAAGTTTAAGTCAGTTTACCTCTTCTCAACCTTGTATGTGCTCACCTTGACAATACCATCTGCTACAGCC
upper sequence: GLYMA11G35080.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 5
---------------------------------------------------------------------------tttcatgtttcttttttttttaacaagggatccaaattttgacagtggaacaagttatacagtaaacattaatacg-gatcatgtgatatgacta--------------ttgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
|||| |||| | | | | ||| || | || | | |||||| | || || | | || || |||||| ||| |||||| |||||||||||||| |||||||||||| ||||| || | | || || | |||| | |||||| ||||| | || |||||||||||| |||
gtaagtcgatcatgattctcacggcaccactttgcttgatcctacgatatcattccatcgattccctcctttttctttcctgttcttcctgctcagatcaaatcattcc--cttccggatcaaatcaagttttttcttacttctttttgcaagaccagatgatatagctaagtttgtggttttcttgcagAGAAATCATGCATGCTATGTGGAAGCCTTCAAAGTTTAAGTCAGTTTACCTCTTCTCAACCTTGTATGTGCTCACCTTGACAATACCATCTGCTACAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaacaagttatacagtaaacattaatacggatcatgtgatatgactattgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
cattaat putative branch site (score: 3)
agtaaacattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcatgtttcttttttttttaacaagggatccaaattttgacagtggaacaagttatacagtaaacattaatacggatcatgtgatatgactattgcagGGAAATCATGCATGCAATGTGGAAGCCTCAGAAGTTCAAATACATATATCTTTATGCAACAGTTTATGTGTTCACCCTCACTCTACCATCTGCTATTGCC
- tcatgtt
- - - - - - - - - - - - - - -atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg