Sequence
atgc intronic sequence ATGC exonic sequence...ttatgcctttatgtgtaatatattgtcatttcaaacccattgacatacactgttattcaatttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
Basic information
species | Glycine max |
transcript | GLYMA18G14670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g05050.3 (Oryza sativa), 3'ss of exon 4
----------ttatgcctttatgtgtaatatattgtcatttcaaacccattgacatacactgtt----attca-atttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
| ||| ||| | | | ||| | | ||| | || ||||| |||| || ||| | ||| | | | | | || | ||||| |||||||| || || || || | || ||| |||||||||| ||||||||||||||| || || ||||||||||||||||| ||| | | | ||
gtaagtagcctgatgtgtttctttaatggaaatttttggaaaagtatgattaatcta-gctgtttgacgttcatatcggttaacttaaaaaataatcttccgcatgcttgttcagGTTATACATTACGAACTCCCAAACACCTCGGAGTTATTTGTTCACAGATCTGGACGAACTGCACGAGCAGGGAAGAAAGGAAGTGCAATTTTAATATACA
upper sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 5
--ttatgccttta--tgtgtaatatattgtcatttcaaacccattgacatacactgttattcaatttgtttgtatgtaaatttttacttggtt-tcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
|| ||| | | | ||| ||| |||| | ||| | | || | | ||| ||| | | | |||| |||| | ||||| ||||||| || | || ||||| ||||||||||| ||||| ||||||| ||||||||||||||||||||||| || | ||| ||| | | | ||
gtttgtgcttccccttctctaagctatctccatt----attttttgttgca-atcaccatgtgcatcatctgt-tgtgtaccctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
upper sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107984_T02 (Zea mays), 3'ss of exon 5
-----ttatgcctttatgtgtaatatattgtcatttcaaacccattgacatacactgttattcaatttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
| | || | | || | || || ||| |||| || | || | | | | || | ||| | |||| | ||||| ||||||| ||| | || || || |||||| | |||||||| ||||||| ||||||||||||||||||||||| || | ||| ||| | | | ||
gtttgtgctccccccttctcaaagtcaaagttatctca--ttcattttttta-atcaccatgtgcatcatctcc-tctactcctcatattgttctccttgttcagGTGATACATTTTGAATTGCCAAACTCGTCAGAGTTGTTTGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
upper sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 5
-ttatgcctttatg-tgtaatatattgtca-----tttcaaacccattgacatacac-tgttatt-caatttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
|| || | || | | | | || ||| || |||| | || | | ||| || || | ||| || ||| | ||| |||| | ||| ||||||||||||| ||||||||||| |||||||| ||||||||||| ||||||||||| || ||||| || |||||||||| ||| ||||| |||
tttttgtttccattctttcacttcttttcaacactttccaaagctatgcatgttcacatgccgttgctttttcttcacatgccgttcttttcttgct---------cagATAATACATTATGAGCTTCCCAATTCCTCAGAGATCTTTGTTCATCGGTCTGGACGAACAGGACGTGCAGGAAAGAAAGGAACTGCAATTCTCATTTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacactgttattcaatttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
cttggtttcctctt CT-rich tract
ttattcaatttgtttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgcctttatgtgtaatatattgtcatttcaaacccattgacatacactgttattcaatttgtttgtatgtaaatttttacttggtttcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-tatgcct
- - - - -tatgtgt
- - - - - - - - - - - - - - - tcaaacc
- - - - - - - - - - - - - - - - - - - - - -catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt