Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
Basic information
species | Glycine max |
transcript | GLYMA20G02350.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02350.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
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----------------------------------------------------------------------------gtaagtagtcctgacattccca--acttgtaaactcttccctcgc---------catttcaaacacagaaccgtttcccttt--tgctgaaaactctcctg--cattatcttc-------agGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG------
upper sequence: GLYMA20G02350.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007683_T02 (Zea mays), 3'ss of exon 3
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataact--tgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
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----------------------------------------------------------------------------------------------gtgggtagtccaagattccagaacgaattagtcactcatgctctcactatttggagatctagatccatttttctcgtcctgaatattctcc-tgtgtgatcttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCGCTGCAAAGTTCGCCGTGGGACAAAGGAAACACTGAG------
upper sequence: GLYMA20G02350.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007683_T01 (Zea mays), 3'ss of exon 3
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataact--tgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
| | | || || | | || | | ||| || | ||| || || || | | | || | || | | || | | ||| ||||| || || |||||||| |||||||| ||||||||||| ||||| |||||||| |||||| | ||||| || ||||| || || | ||| ||
----------------------------------------------------------------------------------------------gtgggtagtccaagattccagaacgaattagtcactcatgctctcactatttggagatctagatccatttttctcgtcctgaatattctcc-tgtgtgatcttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCGCTGCAAAGTTCGCCGTGGGACAAAGGAAACACTGAGGCGAGA
upper sequence: GLYMA20G02350.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G173911_T01 (Zea mays), 3'ss of exon 4
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
|| |||| || ||| | || | | | | || | | | || | | || | | | | | ||| ||| ||||| || || |||||||| |||||||| ||||||||||| ||||| ||||||| | |||| | || || |||||||| || || | ||| |||
------------------------------------------------------------------------------------------------------gtgggtactctaagattccagaacgaattagtcactcgtgctgtc---actatttggaggtctagatccatttttcaggtcctgaatatttttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCACTACAAAGTTCGTCGCGGTACAAAGGAAACACTGAGGCGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
ttctcac putative branch site (score: 2)
tgtcctttatcttt putative PPT
aaaatcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA