Sequence
atgc intronic sequence ATGC exonic sequence...cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDO98830 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 5
---cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcc-cctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
||| || | ||| || | | | | || | | | ||| | ||| ||||| ||||| ||||| || || ||||| | ||||||||||| ||||||||||||||||||| || ||||| ||||||||||| |||||||| ||||| | |
gtatggcaatatgagctctgggagcactcagttcaacatcaacataaaaaaaaatcataattgcgtgatccctaaaatgccttgttgca--ttgctcct-acagCTGCCCTGATGTCCGCTATCTATGAGGAGAACAAGGATGAGGACGGCTTCCTCTACATGACCTACAGCGGGGAGAACACCTTCGGCCTGTTTGTCTGAGT
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os07g32800.1 (Oryza sativa), 3'ss of exon 5
cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
| | || | | | || || | | | | |||| | | || | | | |||||| || || | |||| | | ||||| | ||||| || || ||||||||||||||||||| || ||||| || ||||| ||||||||||| ||||| | | | | |
--gtaaattcattgttct-tgatttgtcattgtcatat-cacc--tacccttttggtttccttatattttgcgcat---------acattctattggcagCTTCTTTGATGTCTGCAATCTACGAAGAGAACAAGGATGAGGACGGCTTCCTCTACATGACTTACAGTGGCGAGAACACATTCGGCTCTGCGTAATTCAT
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 6
-----------------------------------cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtcttt------gctcaccacgtccttgc-gcccctccttgcaacccactc---ctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG--TGC-CGGGGAGCAGCT
|| ||| | | || | | || || || | || | || | | | | || | || | | | || | | |||| || || ||||| | || || ||||| ||||||||||||| || || || ||||| |||||||| ||||||||||| || || ||| | || ||
gtctgaaaatcccttgaatcattttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCCTCTACATGACCTACAGTGGCGAGAACACCTTTGGGCTGCTCTAGGCGCG---
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
-cagcagg-gccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGG--GAGCAGCT
| | | || || | ||| ||| || | | | |||||| | || | | | | ||| |||| || || ||||| ||||||| ||||| ||||||| ||||||||||| || ||||| || ||||||||||||||||| ||||| || | ||| |
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgcccc-ccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGG-GCTGTTCTGAGTGGG-
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgt-ccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG-TGCCGGGGAGCAGCT
| || || | | | | | | ||||| || | || || || | ||| | ||| |||| || || ||||| ||||||| ||||| ||||||| |||||||| || || ||||| |||||||||||||||||||| || || | ||| ||
------gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttt--tcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC-
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------cagcagggccagagccgggcgctgtggcacc----gccgtg-tgcaccgtcgctgtctttgctcacc-acgtccttgc--gcccctccttgcaaccc--actcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG-TGCCGGGGAGCAGCT
| || | | || || ||| | | || | | || || | || || | | || | | | ||||| ||| | | |||| || || ||||| || |||||||| || ||||||||||||| || || || ||||| |||||||| || |||||||| ||||| || ||
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttg-agcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC-
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: Vv10s0116g01700.t01 (Vitis vinifera), 3'ss of exon 5
cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
| || || ||| | | | | | ||| || | || | | || | ||||||| || | ||||| | ||||||||||| |||||||||| || || ||||| ||||| |||||||| || |||||||| ||||| | | | ||
-------gttagtgcaaaatgctataatttagtggcatac--------tgttcttcaaaattgtgtttgtaatatagtttctg--------ttgtcacagCTGCATTGATGTCTGCTATCTATGAGGAAAACAAGGATGAAGATGGTTTTCTCTACATGACCTACAGTGGTGAGAACACATTCGGATTCTGCAAATAGAA
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------cagcagggccagagccgggcgct-gtg-gcaccgccgtgtgcac-cgtcgctgtctttgctcaccacgtccttgcgcccct--ccttgcaacccactcct------------cacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG--TGCCGGGGAGCAGCT
| | | || | | | || ||| || || | | || | ||| | || ||| | || | | | | | | |||| || | |||||||| |||||||| || |||||||| || ||||| || || || | ||||||||||| |||||||||||||| | || ||| | |
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG--
upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S249_49V6.1 (Physcomitrella patens), 3'ss of exon 4
cagcagggccagagccgggcgctgtggcaccgccgt-gtgcaccgtcgctgtctttgctcaccacgtccttg--cgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT-
| | | | | | | |||| || || ||| | | | | | | || ||| | | | || | |||| | |||| || | ||||||||||| || || || ||||||||||||||||| || |||||| | || ||||| || || ||||| ||||| | | | || ||
---ttgattctagtctgtgtattattgcactgctgttgtgtgggatttgttgatgggttacttaattcattgaatgtcgcaccattcaactttgtttgtgcagCTGCTATGATGTCATCCATTTACGATGAACACAAGGATGAGGACGGATTCCTGTACTTTACTTACAGTGGTGAAAACACCTTCGGAGATGTT-ATCAACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
tgctcac putative branch site (score: 2)
cccactcctc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGGGAGCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - -cgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - tgtcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaccca