Sequence
atgc intronic sequence ATGC exonic sequence...atgcgcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
Basic information
species | Glycine max |
transcript | GLYMA15G00510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 1
-----------atgc-gcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
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ttgcttactcaatgttgtatatgtaaaaatatgctggtttctattagagcagagttgcacttgg--agcatatgagtaaaat-----ctttttctcccgttgttca-----gGCAGCTGAATTGGAAATTGAAGCATATCCCTTGTTAGATGAGCTGACATCCAAAATCAGTACACTGAATTTGGAACGTGTACGGCGATTAAAAAGTAGGC
upper sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 1
--atgcgcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
|||| ||| | || ||| | || ||| || | | | || | ||||| | | || | | | | || | | || | |||| || || || || || || || |||||||| |||||||||||||||| || |||||||| || ||||| ||||||| || || || || || ||||
gcatgc-cttgtatataatgatgctgattgccctt-tgatactaataaaaattataaaatcagtacatatgtagtaatgtgtgtttttctgtttctcttcagGCTGCGGAATTGGAGATTGAAGCATATCCATTACTGGATGAACTGACATCCAAAATCAGTACTCTCAATTTGGAACGTGCCCGGCGATTAAAAAGTAGAC
upper sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80900.1 (Arabidopsis thaliana), 3'ss of exon 2
atgcgcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
| | ||||| | || ||| || || | | | | | | || || ||| | ||| |||||||||| || ||||| || ||||| |||||||| || || |||||||||||||| ||||| || || |||| |||| | | ||||||||||
-----------------gtcagtgattgat-tcacaacttattgttatttagtatgctcagcattgagaatagatttt---------ccctttgta---gGCTTCAGAGTTAGAGATTGAGGCATACCCATTATTGGATGAGCTTACCTCAAAGATCAGTACTCTAAACTTGGAGCGTGCTCGTAGACTAAAGAGCAGAC
upper sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 1
-----atgcgcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
|||| | | | | ||| ||| |||| | | | | | |||| || ||| || | | || | | ||||||| || |||||||| || || ||||| || |||||||||| ||||||||||||||||| |||| || ||||||| ||||| ||||| |||||||
tggtcatgctcccacttgtcaaaa----cttagattatcttagcaaagttgaactaccaaaccttgtaa-gtcatctgatctaggcaattatcctaatcaatcagGCAGCTGAATTAGAAATTGAAGCATATCCTCTGCTGGATGAACTTACATCAAAGATCAGTACCTTAAACTTGGAACGTGCACGTCGATTGAAAAGCAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
ataaactaattagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcgcttttgtagaatatttctctttgatattcttgtccatatggctttgataaactaattagtaacattctcccttctgatctggccatttacaaaagGCAGCAGAGTTAGAAATAGAGGCTTATCCATTGTTGGATGAACTGACATCAAAGATCAGTACACTAAATTTAGAACGTGTTCGTCGGTTGAAGAGCAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG