Sequence
atgc intronic sequence ATGC exonic sequence...aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G23670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------aaaatttatttaatgttgaaggccagtgtaaattctgtgataga-gaaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
|||| ||| | | | | | ||| | || | | | || || | | | |||||||| ||| ||||| | |||||| |||||||||||||| || ||||||||||| ||||| || || ||||| |||||||||||||||||||| || || || ||||||||||| |||
gtaagtaagcctgatagggtcatgatcaaatcactttcttatcacttgtaaagttgcattagtcgttatatgttattctattttgtggtaacaccaatgaatgat-attttgtattgaat--tgcagAGATTATGGACTTTGGCTATCCACAAAATCTCTCACCTGAAATTTTAAAACTTTATATCACTCAGGAAGGTGTACGGTCACCATTTTCATCGAAG
upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
---aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttt--tgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
| | || | | | | | || | | || | | || | ||| || || | || ||| | |||| || |||||| |||||||| ||||| || || ||||| | || |||||||| || || |||||||| ||||| ||||| || ||||| ||||||||||| |||
atccagtgtcatctcgtcataatgacc---gcacgtttaattctgaagtcgcctccccagtc-ttcgttaccatgtgcaactaacacc-actgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 3
aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgatt-attacctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
|| || || ||| | || | ||| || || || | |||||| || ||||||||||| ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| || || ||||| ||||| ||
--------------------------------------------------gtattt-tcgtttggtttcatggaaaattcatcacgcttttgaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCGAAG---
upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 3
aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgatt-attac-ctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
|| || || ||| | | | ||| || || || ||| | |||||| || ||||||||||| ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| || || ||||| ||||| ||
--------------------------------------------------gtattt-tcgtttggtttctcggaaaattcatcacacttttgaaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCGAAG---Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151413117|gb|EV282925.1|EV282925EST: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATG AAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
genomic: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATGgtatgtaatt ... ttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
EST:
gi|193522247|gb|FK477766.1|FK477766EST: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATG AAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
genomic: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATGgtatgtaatt ... ttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
ttgtttttt CT-rich tract
aatgattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG