Sequence
atgc intronic sequence ATGC exonic sequencegtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
Basic information
species | Glycine max |
transcript | GLYMA10G43980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
| ||| | |||| | || || ||||||| | ||| ||||| || || |||||||| || ||||| || || |||||||||||||||||||| ||||| |||||||| || || | |||||||||||||| |
gttcgtacaagatcttctctatttatctgcacatgttatgtgttgttttaaatgtgtttcgtttcagtagttggtatagtactgttattacatctgaacaccgtaaaattttggcaaggtttctgcagGCTAATGGCTTGGCGGCTGGGCTCGCAGCTTCTAATCTTATTCTGTATGCATTTGTATACACACCATTGAAGCAAATACACCCTGTAAATACATGGGTTG-------------
upper sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G162776_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
| ||| || ||||| ||| || ||||||| | ||| ||||| || || ||||||||||| ||||| ||||| ||||||| |||||||| ||||| || |||||||| || || | || ||||||||||| |
gttcttgctttctctttgcattcaatatgtatttatattctaccttcttttgaaatttactaaactgtgaagtagatagaaagttg-acactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAACCTTGTTCTGTACGCATTTGTTTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG-------------
upper sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
| || || ||||| ||| || ||||||| | ||| ||||| || || ||||||||||| ||||| || || |||||||||||||||| ||||| || |||||||| || || | || ||||||||||| |
gttcttgctttctctttgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctg-acactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG-------------
upper sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G162776_T03 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
| ||| || ||||| ||| || ||||||| | ||| ||||| || || ||||||||||| ||||| ||||| ||||||| |||||||| ||||| || |||||||| || || | || |||
gttcttgctttctctttgcattcaatatgtatttatattctaccttcttttgaaatttactaaactgtgaagtagatagaaagttg-acactggaactaaacatgcaaaaaattggcaagGTTTGTGCAGGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAACCTTGTTCTGTACGCATTTGTTTATACGCCGTTGAAGCAAATACACCCTGTTAAT-----------------------
upper sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------gtgcttt-gtgtggagggactaacattgctgcttt-atgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
||| || | | | ||| | | | ||||| | |||||||||||| |||||||||||||| |||||||| ||||| || |||| || | || ||||| ||||| ||||| || |||||||| |||| | | ||||||||||| |
gtgaatgtttgtttttttatatgtgatttctttgttttatgaatgggtgattgagagattatggatctaaacttttgcttccacgacaaggttattgcagACTAATATGTTGGCTGCTGGACTTGCATCTGCCAATCTTGTACTTTATGCGTTTGTTTATACTCCGTTGAAGCAACTTCACCCTATCAATACATGGGTTG------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
taatatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT