Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP06643 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 3'ss of exon 1
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
|| ||| | | | | | | | | | || | | | | | | | | || | | | || | || | || |||| | || | || || | || || ||| || | ||||| || || || |||||| |||||||||| || || || |||||||||||| |||||||||| ||| | ||| ||||||| ||||| ||| | |||||
gtgagtcgtcgccctcgtcctcccccctcttgtgctctgctctgctctgctctgtcttcttttgagttttgagctttgagct---cgttgtttgacttgtcgttggcggcgatgag--atgtgactgggtttt-tgttgtggtggggca-acattacagGGCGAGCGATAAATGCCAGAGGGAGAAGCGCAAGACCATCAACGGCGACGACTTGCTGTGGGCGATGGCCACGCTGGGCTTCGAGGACTACATCGAGCCC
upper sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgc-cgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgata----tggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
| | ||| | || | | ||| | | | | | || | || || ||| | | || || | || ||| ||| | ||| || | || | | ||| | | | || ||| | || ||||| ||||||||||||||| ||||||||||||| || || || |||||||||||||||||||||||| | ||| |||| |||||||| || | || ||
----------gtaagtccctcggccgcg-gctgactctgactcttctgtttgcttggcatgttgggaattca-gagtggcgtttcgcaa-accgcactt-tagcttaggtggg-gttttgtgttgacttgt-ctacgtccacgttccttgtctgctgtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC
upper sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
||||||| || | | || |||| | | | | || || ||| | | || || | || || || | | |||| | | || | | | | || | || || || || || ||||||||||||||| ||||||||||||| || || || |||||||| ||||||||||||||| | ||| |||| ||||| || ||| | || ||
gtaagtgcctcag----ctgcggctg------------actcttacttttgcttggcttgttgggaatt-tggagtggcgt----tcagggctttagcttggctggggttt-tgtgttgacttgtccatgtccacgtttttttg-tccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
upper sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgc----actatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
| | | || | || | | | || ||||| | | | ||| || || || |||||||||||||| | |||||| |||| || || || ||||| ||| |||| ||||| |||| ||| ||||||| ||||||||| |||| ||
-----------------------------------------------------------------------------------------------------gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
upper sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
| | ||| | ||| | | ||| |||| | || ||| ||||| || |||||||||||||| | |||||| |||| || || || ||||| ||| |||| ||||| |||| ||| ||||||| ||||||||| |||| ||
------------------------------------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaactatctt-------cttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
tgctgat putative branch site (score: 3)
attctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG