Sequence
atgc intronic sequence ATGC exonic sequencegtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
Basic information
species | Glycine max |
transcript | GLYMA09G40110.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g48140.1 (Oryza sativa), 3'ss of exon 2
gtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaa----catgctaatac-atcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
| | | || | | | ||| || |||| | | || ||| || || ||||| | | |||| ||||||||||| || | | |||| ||||||| || || | |||||||| |||||||||||||||||| |||||||||||||||| |||| |
--------------gtaataagctaaatcttcacatgaatcaatttatgttttacttttaaagaaatggtatggtattaagatctttcctctctgaagGTGGCTAGTTTTGGTGGGTTTTTGCTTAAAGAGAATATCTTGACACTCTCTTTTGCCCCAAGAGATTCACATAAATCTCAAATACAATTTGCTCTGGAGA
upper sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G076841_T01 (Zea mays), 3'ss of exon 2
gtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
|||| | ||| | | | |||| || | | ||||| |||| | || ||| | || || | | |||||||||| ||||| |||| | |||| ||||||| | || | || ||||||||||||||||||||||| |||||||||||||||| ||||| |
gtaatatgttaa----tctgaacttgggaagacttctggttttact----tttaggagttttggtcataatgat---cttttcctctctgaagGTTGCTAGCTTTGGTGGATTTTTGCTTAAGGAGAATATCATGACACTTTCATTTGCACCAAGAGATTCACATAAGTCTCAAATACAATTTGCTTTGGAGA
upper sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
|| ||| | || || ||| | ||| | | | | | || || || | || || || ||||| |||||||||||||| | | || ||| | ||| || || | || ||||| |||||||||||||||||| ||||||| || || || |||||||
--------gtgagaatcatcataag----tctttttatttctcgtttggttctgt-----attgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
tgctaat putative branch site (score: 2)
catcttattttttc CT-rich tract
taatacatcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA