Sequence
atgc intronic sequence ATGC exonic sequence...gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
Basic information
| species | Chlamydomonas reinhardtii |
| transcript | EDP05803 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 6
-----gcggtgaccggaaacccat----gctgggtctga-gcactgggtctgagc-gcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | || ||| || || || ||| ||| || || ||| || | |||| | | ||||| || | || | |||||| ||||| ||| ||||| ||||| ||||||| |||||||||||||| ||| || ||||| ||||||||||||||| | |||||| ||||||| || |
gtaatgtgtcaaatgccaaatcatttcagccaattcagatgcatacggtgtggttagcttggcatttgctgcattgtttg-tgtccatggtggatgaatg---atatgcagGAGAGCGATATCAAATGGGCGTCGCGGTGGGACAGCTACCTGCTGATGACGGATGATCAGATCCACTGGTTCTCCATCGTGAACTCGCTGATGATCGTGC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
--gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgagg-----ccttgaccgcatcctgggctgtccttgctttg---ctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| ||| || | || | | ||| || | || || | |||| | || | | | || || || | | |||| || |||||| ||||| || |||||||||||||||||| |||||| || || |||||||||||||| || || | ||||| | ||||| || |
gtacaa-gactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcc----tgggctgtccttgc---tttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
|| | | | ||| | | | | || ||| ||| || || | || |||| |||| | |||| || || ||| ||||| || || |||||||| || || | |||| || || ||||| ||||||||||||||||||||||| |||||||||| |
---------------gtattgctgattaaaatcttggctaccaat---aaactttcacctcatttgttatgatacgttatggcaagtttgttggtact--ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt-ccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
|| | | | | | || || | | | | | || | || | | | || |||| |||| | |||| || || ||| ||||| || || |||||||| || || | |||| || || ||||| ||||||||||||||||||||||| |||||||||| |
---gt-attgctgattaaaatcttggctactcataaattttcacctca-----ttcattatatgatacgttaagccaaagtttgttggtatt--ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTTTGATGATTGTTC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: AT1G55130.1 (Arabidopsis thaliana), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtc--cttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | | ||| || | || ||||| | | | || | | | |||||| || | ||| ||||| |||||||||||||| ||| |||| |||| || || || || |||||||| || ||||| |||||| | ||||||||||
------------------------------gtaactaatttactctggagaactc--tttatttatgcgctgtaaacatattatgaagtatgaaatatgcagGAGAGTGTTATCAAATGGGCTTCGCGCTGGGACACATACTTGCTTATGAACGATGATCAAATCCACTGGTTTTCAATCATAAACTCGCTTATGATTGTCC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| || | | | | | || | ||| | | | | | | ||| |||| || | | | |||| || | ||| ||||| || || ||||| || ||||| || |||| || || ||||| ||||||||||||||||| ||||| ||||||||||||
----------gtaattctttttcgaaatccttgcttg-tcttctcccatgatacggttt---tttttacttgtttttgccttattatt-------ttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggcc-ttgaccgcatcctgggctgtcc--ttgctttgctggtggcg----acgtgc------agGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | ||| | |||| || || |||| || || | || || ||| || | ||| || | |||| || || | || ||||| || |||||||| || || || || |||| || | ||||||||||||||||||||||| ||||| | |||||||| |
gtgagaaattcgt-ctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: EFJ35060 (Selaginella moellendorffii), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt----ccttgctttgctggtggcgac-gtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | || ||| || ||| || | | |||| | || | | ||||| || | | ||||| ||| | ||||| | || || ||| ||||||||||| |||||||| || ||||| |||||| ||||||| ||||
-------------------------------------------gtgaaagtttttggaaaaattctgcgccttgtaactttgcgtgtttgttttcttttatgcagTTGAGTCCAGTGAGATGGGCTTCGAGATGGGATATGTATCTCTACATGTCCGACGACCAGATCCACTGGTTTTCGATCATCAACTCGCTGATGATCGTCC
upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: EFJ17419 (Selaginella moellendorffii), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt----ccttgctttgctggtggcgac-gtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | || ||| || ||| || | | |||| | || | | ||||| ||| | | ||||| ||| | ||||| | || || ||| ||||||||||| |||||||| || ||||| |||||| ||||||| ||||
-------------------------------------------gtgaaagtttttggaaaaattctgcgccttgtaactttgcgtgtttgttttcttttatgcagTTTAGTCCAGTGAGATGGGCTTCGAGATGGGATATGTATCTCTACATGTCCGACGACCAGATCCACTGGTTTTCGATCATCAACTCGCTGATGATCGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
ccttgac putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
- - - - - -aaaccca
