Sequence
atgc intronic sequence ATGC exonic sequence...ctctttccctctttccttctgtttctttctctttcccacctgaattctttaacacatgtttttatattattatctaatcttatctctacattgatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
Basic information
species | Glycine max |
transcript | GLYMA04G38660.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 5
ctctttccctctttccttctgtttctttctctttcccacctgaattctttaacacatgtttttatattattatctaatcttatctctacattgat---ttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
| | | | | || | | | || | ||| || || || |||| || | | || | || || | | ||||| || | |||||| | || ||||| |||||||| |||||||||||||||| || || |||||||| ||||| || ||||| ||||||
--cctatttgcacccaccatacaagttagtgtaccatgaatgcactctctatca-atattttgctaatggctagttcctttgtttcgttatctgttaatccagAGAATTTCAGAAACAATGGACTTTGAGATTAAGCGATGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT----------
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 3'ss of exon 5
ctctttccctctttccttctgtttctttctctttcccacctgaattctttaaca-catgtttttatattattatctaatcttatctctacattgatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
| | |||| || | | | || || || || || | | || | |||| | | || | || | ||| ||||| ||| || ||| |||| |||||||| | | | ||||| |||||||||| ||| ||||| ||||||||| | || ||||||||||||
tttgctagtgcttttgttttagctgcatggtaatcacagctttcttgcgtactaatactagttggtgctattgg-tgctgttggcactttctgaattccagAGAATTGGGGACACACTAGACTTTGAAATCAGGAGGTGGGCAGCTGGAAAAGAGGGCAACTTACGTGCTTTGTTATCAACTTTACAATAT----------
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G839757_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------ctctttccctctttccttctgtttctttctctttcccacctgaattctttaacacatgtttttatattattatctaatcttatctctacattgatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
| | | | ||||||| | | | | || | | | | | || | || || | | || | | | | | ||| |||||| |||| |||||| | || ||||| ||||||||||||||||||||||||| || || |||||||| ||||| || ||||||||||||
gtaagtaccctgttgtaactcgtaaatacatcttaaattcataatgctgacaatctacatcattaacatataatttgtccttctaatgcactttattggctgctagtgactagttcctcacttcgttgagtt--tgttcaaattgttttgtctgataattccagAGGCTTGCGGAAACACTGGACTTTGAGATTAAGCGCTGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTACAATAT----------
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 5
ctctttccctctttccttctgtttctttctctttcccacctgaattcttta---acacatgtttttatattattatctaatct---tatctctacatt---gatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
| ||| || | | | ||| ||||| |||| || || || | || | | | | | | ||||| | | ||||| ||| || || |||| || ||||| ||| | ||| ||||||| |||| ||| ||||||||||||||| | || ||||||||||||
---------catcattttcagtcagtgattagagcatgccttggccctttagctacacttgcttggatgctgatagcccacttgtttgtttggacattctgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAAGAGGGCAACTTGCGTGCTTTGTTATCAACTTTACAATAT---------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaacacatgtttttatattattatctaatcttatctctacattgatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
tttttatattattatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctttccctctttccttctgtttctttctctttcccacctgaattctttaacacatgtttttatattattatctaatcttatctctacattgatttcagAGGGTTGCTGAAACATTAGATTTTGAAATTAAGCGCTGGGCTGCTGGAAAAGTGGGGAACTTGCGTGCTTTGCTTTCCACTTTACAATATGTATATACTT
- ctttccc
- - ttccctc
- - - - - - - ccttctg
- - - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - aacacat