Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
Basic information
species | Glycine max |
transcript | GLYMA01G35400.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
ttgtgatatttttttcagacattaagttataatctttattg-ccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
|| | | | | | | |||||| | || ||| ||| | | || | | || | || | || | | || ||||| | |||||||| ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||| || ||||| || || || |||
gtgcaagcatataattgtcccctt-gttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
upper sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
||||| | | | ||| || | | | | ||| | || | || | || || | || ||| | ||||| | | || ||||| |||||||||| ||||||||| |||||||||||||| ||||| || ||| ||| ||| || | || || |||||||
-----gtatttcctgccacaccctttcaacaatacatacaa--aacagtgaaaaaaaatga--tttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
upper sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv02s0087g00190.t01 (Vitis vinifera), 3'ss of exon 9
ttgtgatatttttttcagacattaagttataatctttattgccag---tatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
| | || ||| | | ||| | ||||| || ||| ||||| | | |||| | | | | || || ||| | | || ||||| | ||||| |||||||| || || |||||||| |||| || |||||||||||||||||||||||| | || | |||| || |||||| ||
-tttcttaatttatactcttatttacctataaaaaaagttaccaagtttatcaaagttcattgaattttcaaaatctcat--ttctggccataatatcatcagGTGGCTCCCAACGGATGGTCGGAGGGTGAATGCAAGGGCACGGCCGGATGGTTTCCCTCTGCTTATGTAGAAAGGCGTGACAAAGCTCCGGCCAGCGTGA
upper sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ27680 (Selaginella moellendorffii), 3'ss of exon 8
ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
| ||| |||| | | | || | | || | ||| |||||| ||| ||| ||||| ||||||||||| |||||||| || ||||||||||| ||| | ||||| || | | | | || || |||||
------------------------------------------------gtgggtgac--gagccaaagtcattgaatgaatgaacgtttttcttttgcagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG
upper sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ37265 (Selaginella moellendorffii), 3'ss of exon 8
ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
| ||| |||| | | | || | | || | || |||||| ||| ||| ||||| ||||||||||| |||||||| || ||||||||||| ||| | ||||| || | | | | || || |||||
------------------------------------------------gtgggtgac--gagccaaagtcattgaatgaatgaacgtttttctttggcagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
gactgat putative branch site (score: 3)
catttcc putative PPT
tgtatttgtattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtt