Sequence
atgc intronic sequence ATGC exonic sequence...catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcatacatattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
Basic information
species | Glycine max |
transcript | GLYMA10G44110.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaat-ttttgtactgcaaca-tcttacaatcatacat-attatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
| | || | | | | | | | || | |||||| | ||| | || || | |||| || | | | | | | | |||||||||||||| ||||| | ||| |||| || |||||||||| |||||||| ||||||||| |||||||||| || ||| ||||||| |||| |||
---gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 15
--catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcata----catattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
| | | | | ||||||| | | |||| | | || | | | | ||| || | || | | | ||| |||| ||||||||||| || ||||| | ||| ||||||| |||||||||| ||||| || ||||||||| | ||| ||||||||||| |||||||||||| | |||
tgcttattatcgtttttttat----caaaattagtatgtgtcttgttt--ttactcttcttttccctagcttgttccacgcttacaggatcatgacatatatgcagGAAAAGTACGAGGAAGCTATGGCTTCACTTGCCCAAATGGAGAACAGAGCTGTAATGGCAGAAACAATGTTGGAGGCTACACTGCAGTACCAATCTAGCC
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 15
--catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaat-ttttgtactgcaacatcttacaatcatacatattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
|||| || | ||| || || || | | || | | | || | || || | | | | ||| || | |||| ||||| ||||| || | ||| | ||| |||||||| |||||||||| |||||||||||||||||| ||||| | ||||| || | |||||||||| | | |
ttaatgtttgggcatgaatatgtcgcagcat-gtaatgaagcaagtaaatttttgcttgttcagttttatgatccgctgcttgtgtacttactctatt--cagGAGAAGTACGAGGGAGCTATGGCTTCACTTGCTCAAATGGAGAACAGAGCAGTTATGGCAGAAACTATGTTAGAGGCAACCATTCAGTACCAATCTAGTC
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G094951_T02 (Zea mays), 3'ss of exon 1
catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcataca--tattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
| || | | || | |||| | || | | | |||| || | || | | | || | || ||||||||||| || ||||| | ||| ||||||| |||||||||| |||| || ||||||||| | ||| | ||||||||| |||||||||||| | |||
-ttatcgtttttaccagaattagcaaaattagcacgtgtctt-ctttgtactcttcttttaccctagcttgttccacgcttacaggatcatgacatgtgcagGAAAAGTACGAGGAAGCTATGGCTTCACTTGCCCAAATGGAGAACCGAGCTGTAATGGCAGAAACAATGTTAGAGGCTACACTGCAGTACCAATCTAGCC
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
catgtcaatgcctttttatactgctatattatat--ttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcatacatattata-ttgac--agGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
||| | || | ||| | |||||| || || | | | || || | || | | | |||| ||| || ||||||| || || ||||| ||||||||| ||||||||||||||||||||||| |||||||| || ||||| ||||| || |||||||| |||| |||||
-----agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
upper sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 15
-catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaatttttgtactgcaacatctt-acaatcatacatattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
||| ||| | | || | | | || | | || ||| || | ||| | | || ||| || || |||||||||||||||| || ||| || || || || |||||| |||| |||||||||||||| || ||| ||||||| || |||||||| |||| |||||
ttatgaggatgtcatcttgttagagtttctt-tgtctcagtatacacttattcgaggcgacacaaaaagttatcctcagtatgata-atgctaatggtgtagGAAAAGTATGAAGAGGCTGTTGCAGCTCTCGCGGAGATGGAGGAGAGGGCAGTTATGGCAGAGTCCATGTTGGAGGCGACTTTGCAGTATCAATCTGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgatgaatttttgtactgcaacatcttacaatcatacatattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
atcttac putative branch site (score: 3)
ttacaatcatacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcatacatattatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - -caatgcc
- - - - - - - - - tactgct
- - - - - - - - - - - - - - - - - - - - - -cacaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacat