Sequence
atgc intronic sequence ATGC exonic sequence...atttccattattcttttgtttctttggaacatactaatcccaaacagctgactggatactatatttttggctaattttgtcttcaaccttgcactcacagGAAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
Basic information
species | Glycine max |
transcript | GLYMA09G39090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 1
atttccattattcttttgtttctttggaaca--tactaatcccaaacagctgactggatactatatttttggctaattttgtcttcaaccttgcactcacagGAAAAAGGAAAAGTAAAG---------------TTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
| ||| | || || | ||| ||| || || | | | | | | | || |||| | || | || | | | | ||| | || ||||||||| || ||| |||| ||| |||||||||||||||| |||||| || |||| ||||||||||| | || |
--cttcatggtgtttctgggttactggcacatgtaatattggcgatgaagttaaagcatgatatagatctgaccttgttaattgtaatgacattatgtgaagGTTACTGGGAAAGTAAAGCGTCCTTCTATTGTATTTCCTTCTGCTGCAAGAAGAATGGATACTCTCAATGATCTATTAGCAGCAAGTGATCTAGTTTCGC---------------
upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
atttccattattcttttgtttctttggaacatactaatcccaaacagctgactgg-atactatatttttggctaattttgtcttcaaccttgcactca-cagGAAAAAGGAAAAGTAAA------------GTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
||| ||| | | ||| | | ||| ||| ||| || | |||| |||||||||| |||| || | | |||| ||| |||||| ||| || ||||| || || ||||||||||||||||| ||||||||||| ||||||||||| ||| | || || |
-tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtcta-aaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC------------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|8283239|gb|BE020800.1|BE020800EST: CTCGCAGCTTGGCCTTCAAAATGAGCGTGCTGTATTTCGATGCTCGCGCG GAAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTT
genomic: CTCGCAGCTTGGCCTTCAAAATGAGCGTGCTGTATTTCGATGCTCGCGCGgtaccttctt ... gcactcacagGAAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctgactggatactatatttttggctaattttgtcttcaaccttgcactcacagGAAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
ggctaat putative branch site (score: 3)
atactatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttccattattcttttgtttctttggaacatactaatcccaaacagctgactggatactatatttttggctaattttgtcttcaaccttgcactcacagGAAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - -ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - gctgact