Sequence
atgc intronic sequence ATGC exonic sequence...gttttttcatggtgtgtgattttttatgtgatggagcttatcatctgctattatacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
Basic information
species | Glycine max |
transcript | GLYMA04G06810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 1
gttttttcatggtgtgtgattttttatgtgatggagcttatcatctgctattatacat-----ttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
| | || | || | || | || | | |||| | || |||| || | | | | || | | || || ||||| | || ||||| || | || || || ||||| ||||||||||| |||||||| || || ||||||||||||||||| |||| || ||||| |||| |
--tgacccctgtgttactccttatcttggaaatgaacatgtcattgtgtttttcacatggcagcccttcttgtggactctaacatacttctc-ttaat--tgcagACACATTATGTGTTGCTTCTTTGCTCATTCAAGGAACAACTTCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTGATGGGGTGCTGGGAACTTGAAC
upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
------gttttttcatggtgtgtgattttttatgtgatggagcttatcatctgctattatacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
||| || || || || ||| || | ||| || | ||| | | | || || |||| || | ||||| |||| ||||| || | || ||||| ||||| |||||||| || || ||||| || || ||||||||||||||||| |||||||| ||||| |||| |
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaa-aatgtttttttttct-----tgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
gttttttcatggtgtgtgatttttt---atgtgatggagcttatcatctgctattatacatttacaactgacaattttgat-----attttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
|| | | ||||| | | | | || ||||||| || || | | | | || | | | | | || | | ||| | || ||||| || | |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||||||||||||||||| | || |
--------ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 1
gttttttcatggtgtgtgattttttatgtgatggagctt----atcatctgctat---tatacatttacaactgacaattttgatattttcttaattgat-gctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
| || | |||| || | | | | |||||||| | | | ||| ||| | |||| | | || || | ||| | |||||||| || | || || || ||||| |||||||| || |||||||| || || ||||||||||||||||| |||| ||| |||||| |||| |
--------tttgtctaggattccgtacatagttaacatcttgcatcatctgttttggccaggtattcctgttctcagattctaatatgtcactgttttattattacagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAACTCCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC
upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 2
gttttttcatggtgtgtgattttttatgtgatggagctt----atcatctgctatt---atacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
|| | || | | || | || | | | | |||||||| | || | | || ||| | |||| ||| | || | ||||| | |||||||| || | || || || ||||| ||||| || || |||||||| || || ||||||||||||||||| |||| ||| |||||| |||| |
------tctttgtctagggttctgtacatagttaacatcttgcatcatctgtttttgccaggccttcttgttcccagattctaatatattcctgtttt-tattgcagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAGCTGCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctattatacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
aattttgatattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttcatggtgtgtgattttttatgtgatggagcttatcatctgctattatacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT