Sequence
atgc intronic sequence ATGC exonic sequence...tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
Basic information
species | Glycine max |
transcript | GLYMA05G37870.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
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-----------------gtgagtatcgtgtgatt-tgttttttcaacatgatcagca---gtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
upper sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagccta----aatagtaa-gtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
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gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttt-tagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
upper sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 4
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
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---------------gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataattttatgtttttgtttcttagGATGCA-------AATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
upper sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
| ||| | || | ||| | || | | | | | | || |||| || | | || ||||| | ||||||||||||||||||| ||| ||||||| |||||||| ||||| | |||||| || ||||| || || ||||| || |||||||||||||
-------------gtaagta--tgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
tgttgac putative branch site (score: 3)
tgttgactgtcctttt CT-rich tract
tttttctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-gggtgga
- - - - gctgtgg
- - - - - - - - - - actgcta
- - - - - - - - - - - - - - - - -tgcgtgt
- - - - - - - - - - - - - - - - - - - - - - -gcctaaa