Sequence
atgc intronic sequence ATGC exonic sequence...gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP02440 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGC---GCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
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--------------------------------gtatgcaatttccttgaactataaaagctcgctttttcatatatttggac-tgtaataactgcaacatatttgttgagcagATGATGTGGCGGCTTAATTTCTTTGTGGTGTTCTGTTGTATTGTACTTAACAACAGTTACATGTTATACTACATCTGCCCCATGCACACTCTTTTCACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGC---GCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
| || || | | | ||| | | | | || ||| | ||||||||||||||| || || ||| | ||| | |||| || | || || |||||||| |||||| | |||||||||||||||||||||||
-----------------------------------gtatgcaatttccttgaactataaaagctgactttttaatatttggtctgtactaactgcaacatattggttgagcagATGATGTGGCGGCTTAATTTCTTTGTGGTGTTCAGTTGTATTGTACTTAACAACAGTTACATGTTATACTACATCTGCCCCATGCACACTCTTTTCACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
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--------------------------gtaagagctatgtcctcccggcttttttcttatttttg-gctgtcacctacttgaaattctaacatattcttggtct---acagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
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-------------------gtaactgcccctaaatctcttaagtttg-attcatggagttcca----tccatgatattctgattctaatagtaagttttttgttgaacagATGATGTGGCGGCTTAATTTCTTGGTGTTGTTTTGCTGTGTTGTCCTTAATAACAGCTATATGCTATACTACATTTGCCCCATGCACACTCTTTTCACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 2
--gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcact----cgtctcatcccc-acgcttcccgcttcccgac--accccgcggttccct-cagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
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gtgaccttgttaattctgaactgtttcatcatttctctattagaagtgatattgttccttttcattttctatatttcaattttgataatttaggatgtgaatctttactttctaatgcagATGATGTGGCGGCTAAATTTCTTTGTGGCATTTTGCTGCATTGTTCTTAACAATGACTACATGCTATACTATATCTGCCCCATGCACACGCTTTTCACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
|| || | || ||| | | | || | | | | || || | | | | | || | ||| || | | |||| | ||||||||||||||| ||||| ||| |||| ||||| | ||| | || || ||||| ||||||||||||||||||||| || ||||||||
---ttcgc-gatctgctttgagggtg----tggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgat-gatttg-gcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ29067 (Selaginella moellendorffii), 3'ss of exon 7
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
||||| | || | | | || | | ||||||||||||| | |||||||| | ||| ||| ||| | || |||||||||||||||||||||||||||||||| || ||||| |||
-----------------------------------------------------------gtaactgcttctttgcactcgtaagttcatgctttgtgaacgcacttgcagATGATGTGGAGGCTCAACTTTCTTGTGACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTCTACTACATCTGTCCTATGCATACCCTCTTCACAT
upper sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ17601 (Selaginella moellendorffii), 3'ss of exon 6
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------
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-----------------------------------------------------------gtaactgcttctttgcactcgtaagttcatgctttgtgaacgcacttgcagATGATGTGGAGGCTCAACTTTCTTGTCACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTTTACTACATCTGTCCTATGCATACCCTCTTCACATMapped 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|16434370|gb|BI999596.1|BI999596EST: TTCGGCAACTTTTCTTACTACTACAAAACCGGGGACTTCTGCATTGGCCG ATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGT
genomic: TTCGGCAACTTTTCTTACTACTACAAAACCGGGGACTTCTGCATTGGCCGgtgagcgctg ... gttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC
ttccctc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC
- gtttgct
- - - - - -cacgcgc
- - - - - - - - - - - - - - - - - - - cacacct
- - - - - - - - - - - - - - - - - - - - - - - gcactcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacccc