Sequence
atgc intronic sequence ATGC exonic sequence...ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
Basic information
species | Glycine max |
transcript | GLYMA08G03760.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
-ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtattaacaccttg--gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
| || | |||| | |||| ||| |||| |||| | | | | ||| ||| | | | || | | | ||| || |||| || || | |||||||| || ||||||||||| |||||| ||||||||||||| || || || ||||| |||| ||||| ||||| || |
ttcagcagttaaatagtatcatcttttgatttttgtctatttaccaaccaagcatgat--gagttgacagggtaatga-atttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
upper sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 5
--ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtat-taacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
| | || || | | || | | |||||| || | || || | || || |||| | || | | | || ||| | || || || | ||||| || |||| ||| |||||||||||| | ||||||||||| ||||| |||||||| | |||||||| ||||| || |
tactgtggttactatat-gttcatctcttggccttgttttattttttaccaaagaaggccagta--aattgactcgttactcatgtttatcaaactgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA
upper sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtat-taacaccttg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
| || ||||| | || ||| | | |||| | | | || | | ||| | | | | || | | | ||| | || ||||||| || | |||||| ||||||| ||||||||| || |||||||||||||||||||| || ||||||||| |||||||||| ||||| |||||
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
upper sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 5
ccgacattgaaattttggtccattttcattcttgt--tgatttcctaga-ttgtctttgctagaggcattttaccaattacactagtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
| | | | || | | | || ||| | ||| ||||| | | | | | |||| || || | | || | | |||||||| ||||| | |||||||||||| ||||| |||||||| || ||||||||||||| ||||| |||||||| | || || || ||| | |||||
-atatttgtatacacctgttccctgtaatggttgaagtatttttctagaatcatgtagtttttttgtgctttatcatgtatattctggtt--ctctaatacagGTTGGGGTGGATAGAATGCATAAAGACAGCAAGTATGTATTATTCCTGGATGATGATGTCAGGCTGCATCCTGGGACCATTGGGGCCCTCGTTGCTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgtctttgctagaggcattttaccaattacactagtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
tattaac putative branch site (score: 1)
tagtattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcattt