Sequence
atgc intronic sequence ATGC exonic sequence...cctgtgtgagatcatctagaaaagtcatctccttttcttccagcatctcactgactcactgactttttcgctttctcattggcttctctcttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ13690 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ13690 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA05G10100.1 (Glycine max), 3'ss of exon 1
cctgtgtgagatcatctagaaaagtcatctccttttcttccagcatctcactgactcactgactttttcgctttctcattgg-cttctctcttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT
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----------gtcattcattaattctacaagctggttttgtagggttgagttaggtc--caaaatccacattctaagatttgtcatctttgtttaatgcagGGCGTGTGTTTCCACCGCGTGATCAAAGGTTTCATGATCCAGGGCGGCGACATCTCCGCCGGGGACGGAACCGGCGGTGAATCAATCTACGGCGCCAAGT
upper sequence: EFJ13690 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G20430.1 (Glycine max), 3'ss of exon 1
cctgtgtgagatcatctagaaaagtcatctccttttcttccagcatctcactgactcactgacttt---ttcgctttctcattggcttctctcttgcaa-acagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT
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----ggttgagttatgtaaaaaatccgcattctaagatttgtatggttgagttaggtccaaaatccgcattctaagattttttggcgtcttttaattattgcagGGCATGTGTTTCCACCGCGTGATCAAAGGGTTCATGATCCAGGGCGGCGACATCTCCGCTGGGGATGGCACCGGTGGGGAATCAATCTATGGCGCCAAGT
upper sequence: EFJ13690 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP09953 (Chlamydomonas reinhardtii), 3'ss of exon 3
cctgtgtgagatcatctagaaaagtcatctccttttcttccagcatctcactgactcactgactttttcgctttctcattg--gcttctctcttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT----------------------------
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--------------tct-gctccccccccccgcaccctccgttcatcgccgctataccctggcatccatgcctgctccgtgctgcccccccccttcaaac---------ccctccgccgccc------agACTTCATGATCCAGGGCGGCGACTTCACCAACGGCGACGGCCGCGGCGGCGAGTCCATCTACGGCGACCGCTTCGAGGACGAGGCCTTCACGCTGCTGCAMapped 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|169074129|gb|FE482374.1|FE482374EST: GCACTGGCGAGAAAGGCGTCGGTTCTTCCGGATATCCGCTCCATTACAAG GGCGTGTCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGAC
genomic: GCACTGGCGAGAAAGGCGTCGGTTCTTCCGGATATCCGCTCCATTACAAGgtatctgttt ... ttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcactgactcactgactttttcgctttctcattggcttctctcttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT
cactgac putative branch site (score: 2)
ctttttcgctttctca CT-rich tract
acttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgtgtgagatcatctagaaaagtcatctccttttcttccagcatctcactgactcactgactttttcgctttctcattggcttctctcttgcaaacagGGCGTGGCTTTTCACCGCGTCATCAAAGGCTTCATGATCCAAGGCGGCGACTTCACCGCTGGCGACGGCACCGGCGGCGAATCCATCTACGGCCTCAAGT
- - - - - - - - tagaaaa
- - - - - - - - - - - - tcatctc
- - - - - - - - - - - - - - - - ttttctt
- - - - - - - - - - - - - - - - - - - - cagcatc