Sequence
atgc intronic sequence ATGC exonic sequence...taaaaaaaattgttagtcagaacatttctcttgctccaccttacaagtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatgaatagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
Basic information
species | Glycine max |
transcript | GLYMA07G36000.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 4
----------taaaaaaaattgttagtcagaacatttctctt----gctccaccttacaagtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatgaatagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
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gtctgtgattttgtttcccctttcagcaactacacttctgatctacgaacaacccacctcagcttcttgtttctcactgaatccgttggacaaaaaaaaat-ataaattaaaagGTCATTGCTGGATGCTTGTCGGAGGAAGAGATCAGAGGGCTGAAGGAGATGTTCAAGAGCATGGACTCTGACAACAGCGGCACCATTACCGTCGATGAGC
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 3
-taaaaaaaattgttagtcagaacatttctcttgctccaccttacaagtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatgaatagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
||| || ||| || ||| ||| | | | | |||| || ||| | | | | ||| | ||| | || || |||| || || || || ||||||| |||||||||||||| || || || |||||||| || |||||||||||||||||||||||||| || ||||||| |
gtaattaacattcttc-tcaaaaccatatatgtattgtaataaacaa---tgcgagtct----tttggtctatatatctcattggcatcatcaacaaacagGTGATAGCCGGGTGCTTATCAGAGGAAGAAATCATGGGGTTAAAAGAGATGTTCAAAGGAATGGACACTGACAACAGTGGAACCATAACTCTTGAGGAAC
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 4
-taaaaaaaattgttagtcagaacatttctcttgctccacctt-acaagtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatga-atagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
| | || | | | ||| |||| || || | ||| | | || | | | ||| ||| || || | | ||||| ||||||||||||| ||||||||||| ||||||||||||||||||||| ||||||| ||||| ||||||||||| || ||||||||||| ||| |||| ||||
tcactcatggttctgaaactgaaactttc---tggtcaatcttgatgatctttacaaattttgaggaaatttctttattgtttattttctcaaaatgttgcagGTCATTGCTGGCTGTCTATCAGAGGAAGAAATCATGGGATTGAAGCAAATGTTTAAGGGCATGGACACTGATAATAGTGGAACCATAACACTTGAAGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatgaatagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
acataac putative branch site (score: 3)
ataacattaaaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaaaaaattgttagtcagaacatttctcttgctccaccttacaagtttgaaagtgtatgatcaaagcaacataacattaaaacattacaaatgaatagGTCATTGCTGGATGTCTATCAGAAGAAGAAATCATGGGATTGAAGGAAATGTTCAAGGGGATGGACACTGACAACAGTGGAACCATTACAATTGAGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
-aaaaaaa
- - - - - - - - - - - - - - - - -ctccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacatt