Sequence
atgc intronic sequence ATGC exonic sequence...tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG
Basic information
| species | Chlamydomonas reinhardtii |
| transcript | EDO99380 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGT--GCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| || | | || ||| | | | | | ||| | | || | ||||| | |||||| | | || | || ||||| | ||| ||| || || || |||||||||||||| |||||||||||| |||||||||||||||| ||||||||||||||||| |
---------gtaagcccagcgccctgcagggagcacgtaacgctctct-ctggtcggccgggcccacctgtcagag--ccatccaa----ttgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os03g03370.2 (Oryza sativa), 3'ss of exon 3
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattct-tcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagAT--------CGGCGGCGTGTGC-TTCGGCGC-GGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
|| | | || | | | |||| | || | | ||| | | | |||| | | ||||| | |||| ||| ||| || || |||||||||||||| || || ||||||||| |||||||||||||||| |||||||||||||| ||||
-----------------------------------agcgtttctttttgttcaatttgattgccaaggttgaatttttgtgatctggggctctgggcagagatgatccaagtgctgacgtgtccgttcgccgcagGGACTCGGGATCACGCTGTTCGGGATGGCGTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCGGTGGGGCCCATCGCCAACGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os10g38940.1 (Oryza sativa), 3'ss of exon 2
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
|| || || ||| ||| | | | || | | | ||| | | | | || | | || || | || | || | | ||| |||| || ||||||||||| || || ||||||||| |||||||||||||||| ||||| |||||||||||||
------------------gtcacgtcgtggtcgggggcgtatccgttttgaggctcttctttatcgtctga-tgggtgacgtgtcacgtggttggcgctga-cgtggccgcgcgcaacag-
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G152135_T06 (Zea mays), 3'ss of exon 3
-------------------tcatactacgcgtgctccatctcg--ggcggggcggtggcat--cccattcttcccatttcccaccactacctgcctacctcccatcccaaaccc---ccaacccagATCGGCGGCGTGTGCTT-CGGCGC-GGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| ||| || || | | | | | || ||| | || |||| || || || ||||||| | ||| | || | | | | ||||| | | | | ||| ||||| || |||||||||||||| |||||||||||| |||||||||||||||| ||||||||||| || || |
gtaagctagctagctagccacggactgtgcctggttagtttagttagttggttggtcggatgacccacctctctcagcggtggtgcctgcctgcctgtcagccacgggggatccgactgtgatctcaccctccacgtgtcttcatgtcacagGGCCTGGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCGACGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G164318_T01 (Zea mays), 3'ss of exon 3
--------------------------tcatactacgcgtgctccatctcgggcggggcggtggcatcccattctt-cccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| | | || || | || || || | | || | || || | || | || | | | | | || | | || | || | | || ||| || || || |||||||||||||| |||||||||||| |||||||||||||||| ||||||||||| || || |
gtaagctagccacgtacagtatctcggtgtgttgtgtgt-ctggttagttggttggctggctggacccagctgttgcctggtaggcagggtggctggcgtcagccacgtatccgactgtgatctcaccctccacgtgtcttcctcccacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G090051_T02 (Zea mays), 3'ss of exon 2
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| | || ||| || | || || | | | | | | || || ||| || | | | | | ||||| || || ||| | || ||||| |||||| ||||||| || |||||||||||| | ||||||||||| || ||||||||||||||||| |
-------gtacacggtcttcctctggtgtggtggccaaggcacgtgcacgct-----------cggccggctctgctctgctctga----cttggctctggccggcgtcgctcgcatcgcagGGG--CTGGGGATCACGTTGTTCGGGATGGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGCTTCCCCGTCGGGCCCATCGAGAACGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G382534_T01 (Zea mays), 3'ss of exon 3
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacc-cccaacccagATCGGCGGCGTGTGCTTCGGCGC-GGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| | ||| || | | ||||| || || | | | | | | | || || || | | ||| ||| ||||| |||||||| ||||| || |||||||||||| | ||||||||||| || |||||||| |||||||| |
------------------------------------gtgagtctctctgccgacgacgatccactctttgtgcacacgctagcttggccggttcttctctgacgtgcctcgcggcgtcgctcgcagGGGCTGGGGATCACGCTCTTCGGGATGGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGTTTCCCCGTCGGCCCCATCGAGAACGTGCCCTACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ08548 (Selaginella moellendorffii), 3'ss of exon 4
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| || || | | ||| | | ||| ||||||||||| | ||||| || ||||||||||| | ||||||||||||||||||| | || || || |
--------------------------------------------------------------------------gtaagtaatagaagtatttcttgtagctttgaaaatattgcatt--ccagGGCCTGGGCATCACCATCTTCGGGATGGCCTACATGTTTGTTCACGACGGCCTGGTGCACCAAAGGTTTCCAGTTGGCCCACTGGCCGATGTACCATACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ13409 (Selaginella moellendorffii), 3'ss of exon 4
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| | | | ||| || | | || | ||| ||||||||||| | ||||| || ||||||||||| | ||||||||||||||||||| || || | || |
---------------------------------------------------------------------gtaagtaatagaagcatttcttgtaactttgaa-aatattgcatatcacgtca-gGGCCTGGGCATCACCATCTTCGGGATGGCCTACATGTTTGTTCACGACGGCCTGGTGCACCAACGGTTTTCAGTTGGCCCACTGGCCGATGTGCCATATT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ11185 (Selaginella moellendorffii), 3'ss of exon 4
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| || || | | ||| | | ||| ||||||||||| | ||||| || ||||||||||| | ||||||||||||||||||| | || || || |
--------------------------------------------------------------------------gtaagtaatagaagtatttcttgtagctttgaaaatattgcatt--ccagGGCCTGGGCATCACCATCTTCGGGATGGCCTACATGTTTGTTCACGACGGCCTGGTGCACCAAAGGTTTCCAGTTGGCCCACTGGCCGATGTGCCATACT
upper sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ11878 (Selaginella moellendorffii), 3'ss of exon 4
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------
| || | || | | ||| | ||| ||||||||||| | ||||| || ||||||||||| | ||||||||||||||||||| || || | || |
--------------------------------------------------------------------------gtaagtaatagaagcatttcttgtagctttgaaaatattgcat--atcagGGCCTGGGCATCACCATCTTCGGGATGGCCTACATGTTTGTTCACGACGGCCTGGTGCACCAACGGTTTTCAGTTGGCCCACTGGCCGATGTGCCATATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG
ccccc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGTGCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG
tcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccaaa
