Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP06387 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os01g59730.1 (Oryza sativa), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
|| | ||| ||| | | || ||| || || ||| | | | |||| ||| | ||| | | ||||| || |||| |||||||||| | |||| |||||| | ||| ||||||||||||||| ||||||||||| || |||||||||||| ||| |||||||| |||
------------------gtggaaaacctaagcttttat-ttggttttgaaagttcttgctgtg--tggctttgtctcttggtgtgggcgtttgatcga--tgggtgggg-----tgttcgcg---gtgttttg--------cagAAGAAGAACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
||| || || | | || | || | || ||| | ||||| | || | | | | | | | | | ||| | | | ||| | | | | | ||||||||||| | ||| ||||||||| | ||| ||||||||||||||| ||||||||||| || |||||||||||| ||| ||||| ||||||
----gtaaggttcctg-atcgattgcgcctccctccccctcctcgtcg------cgctctc-ccgctgcgcatct--caccatttcgttgcgatgtttttgctggtttctga--ttggtgggttgtg------gcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os01g16890.3 (Oryza sativa), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggc----tacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttg-----tgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
| | | | || | | | | || || || | |||||| || | | |||| | || || | | | | | || | | || || || |||||||||| || ||| ||||||||| | ||| ||| ||||||||||| ||||||||||| || |||||||||||| ||| | |||||| |
---------gta-acgttgtcctcctcccggtctctccctccatcacctcggtccgccgcgcaagcgagcgagcgagcgagatcctgcatttctcatggcgctaacgcctctctgttcgtcgtggtgatggtgtgatggtggttgtgtttgcagAAGAAGTCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G044137_T01 (Zea mays), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcg--ctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
|| ||| || || | || | | || |||| |||| || | | | | |||| | |||| | || || | | ||||||||||| | |||| ||||||| | ||| ||||||||||||||| ||||||||||| ||||||||||||||| ||| ||||| ||||||
---------------------------------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtg------aattttcctgtgatgttga---ttggtctcccgttggtttcgatc-tatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcg--ctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG---
|| ||| || || | || | | || |||| |||| || | | | | |||| | |||| | || || | | ||||||||||| | |||| ||||||| | ||| ||||||||||||||| ||||||||||| ||||||||||||||| ||| ||||| ||||||
---------------------------------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtg------aattttcctgtgatgttga---ttggtctcccgttggtttcgatc-tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G027728_T01 (Zea mays), 3'ss of exon 1
----------------------------------gtgcgtaggg---cagatgcagtagcaaaactagccgcagccgtcaaaacggagagtc-gccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtact--ttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
| | || | | | | | | | || | | | ||||| | | | | | || | | | | | | || || ||| | | || || | | || | ||||| ||||||||| || ||| |||||||| | ||| ||| || ||||||||||||||||||||||| |||||||||||| ||| | ||| || |
gtaacgacccctaactccacgctctctccctgtggagtttacgttttcccacactttcgtctatctgtctcctttttttctcacggaaaatgagattctgctgc--attgcgctgggccacgtatctgggcttcggttctaggctctaacactgcgttgttggtgtggtggttgtgtttgtgcagAAGAAATCCACGGACAACATCAATAACAAGCTGCAGCTTGTTATGAAGAGTGGCAAGTACACTCTCGGCTACAAGACCGTCCTCAGGACTCTCAGGAACT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G050460_T02 (Zea mays), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
| | || || || || || || || | || || | ||| | || || | | ||| | || | | || | || | | |||||||| ||||||| || ||| ||||||||| | || ||| ||||||||||| ||||||||||| || ||||||||||| ||| | |||||| |
------------------gcaacatgtcttgctgctgcattccaagt----attcat----gtttccagtcttgcaatttatgtt--cta-------agctctgtttttcgtttttcgttgttggt----tttgtgca------gAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT
upper sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 3'ss of exon 1
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcg--cgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACC-TGCCTGAAGACCCTGCGCTCGG
| | | || | | || ||| | | || | || | | | | || ||| | ||| | | | | | | || ||| | | | ||||||||||| || || ||||||||| | || || || ||||||||||| ||||||||||| || |||||||||||| ||| | || |
-------------------------------gtacggacatcgtattcgttgttccccgatcttattt-tcaacttctctacgat--tcaagagatgtaat---gcatttcattttgtttgattttgtgttgttttggaaatcacagAAGAAGACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
tattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA