Sequence
atgc intronic sequence ATGC exonic sequence...ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcaccatacccccctgccgccgctgccgctggccctccgccgcatgtggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDO97224 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 3'ss of exon 12
ccggctcccggcgtccttagtccat--gcaacca-atctcttctcactcaccatacccccctgccgc---cgctgccgctggccctccgc---------cgcatgtggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
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-------------tccttaatgcaaagggaattgcaagtgttctc-caaattatatcctgttgatgcgagtggttttgttgattaactgatttcaaaaacgtatttgggtgc-agGTGTGTGTGTCGACGACGAACAGGAATTTCCCCGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCTTCGCCGTTCACCGCGGCGGCTTCAGCCC
upper sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcaccatacccccc-tgccgccgctgccgctggccctccgccgcatgtggccgc-cagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
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--gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
upper sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcacca--tacccccctgccgccgctgc-cgctggccctccgccgc--atgtggccgc-cagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
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------cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
upper sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: GRMZM2G133988_T01 (Zea mays), 3'ss of exon 9
-----ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcaccatacccccctgccgccgctgccgctggccctccgccgcatgtggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
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gtattatagagcttgttgtcatttgaaactacaaggaaaacag---caagtgctctgaaattctagt-ttgttgacacatggatctggtaacctggatgtgc-agGTCTGTGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGGCACAAGGAAGGGAAAATCTACCTGGCGTCTCCCTACACCGCGGCTGCCTCAGCCCMapped 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|16431497|gb|BI996723.1|BI996723EST: CCTGCCTGGGCGGGCCGCGCGACACCTTCGCGCGCATGAACGAGCCCGAG GTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCAC
genomic: CCTGCCTGGGCGGGCCGCGCGACACCTTCGCGCGCATGAACGAGCCCGAGgtgagcaccc ... tggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccatacccccctgccgccgctgccgctggccctccgccgcatgtggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
cactcac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcaccatacccccctgccgccgctgccgctggccctccgccgcatgtggccgccagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC
- - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - caatctc
- - - - - - - - - - - - - - - - - - - - -cactcac