Sequence
atgc intronic sequence ATGC exonic sequence...aatgtctgggaaatttcattcctgttaatttgttaggttgtccttgcttgattcattttaccaacgacactagtattacatagtattggcacctgggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
Basic information
species | Glycine max |
transcript | GLYMA16G08510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 5
---aatgtctgggaaatttcattcctgttaatttgttaggttgtccttgcttgattcattttaccaacgacactagtattacatagtattggcacctgggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
|| | | || | || | ||||| || | || | | | || ||| || ||| | | || ||| | || || || | ||||| || |||| |||||||||||||||| | ||||||||||| ||||| |||||||| | || ||||| ||| ||||
tactgtggttactatatgttcatctcttggccttgtt---ttattttttaccaaagaaggccagtaaattgactcgttactcatgtttatcaaactgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------aatgtctgggaaatttcattcctgttaatttgttaggttgtccttgct-tgattcattttaccaacgacactagtattacatagtattggcacctgg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
| | | ||| | | | | || | || || || | | |||||| | || | | | | |||| || | || ||||||| || | |||||| ||||||| ||| ||||| || ||||| |||||||||||||| || ||||||||| |||| ||||| ||| || |
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 5
aatgtctgggaaatttcattcctgttaat--ttgttaggttgtccttgcttgattcattttaccaacgacactagtattacatagtattggcacctgg-gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
|| | || | |||| |||| ||| || | || | | || | ||| | | || || ||| | | | || |||||||| ||||| | |||||||||||| |||||||||||||| || | ||||||||||| ||||| |||||||| | ||||| || |||||| || |
-atatttgtatacacctgttccctgtaatggttgaagtatttttctagaatcatgtagtttttttgtg-ctttatcat-gtatattctggttctctaatacagGTTGGGGTGGATAGAATGCATAAAGACAGCAAGTATGTATTATTCCTGGATGATGATGTCAGGCTGCATCCTGGGACCATTGGGGCCCTCGTTGCTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgattcattttaccaacgacactagtattacatagtattggcacctgggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
gcttgat putative branch site (score: 5)
tattacatagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtctgggaaatttcattcctgttaatttgttaggttgtccttgcttgattcattttaccaacgacactagtattacatagtattggcacctgggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
-atgtctg
- - - - - - - - cattcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaac