Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtactctgcgcatttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP09951 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 1
----------------------------------gtgcgtactctgcgcatttcctttacaacgacaacgc-ctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
| | | | | || | | | | || | | || | | || ||||| || |||||||||||||||||||||||||| ||||||||||| || | ||||| | ||||| || ||
gcaatgtttcagttttaatacttatcttaaaatgtttcagttttaatacttatcttatctggtcgttatgttctcatgatttattctattttgcgaacagGCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTG
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AC166636.1_FGT008 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtgcgtactctgcg--catttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
| | || || | | | | | || | ||| | ||| || | ||||||| || ||||| || ||||||||||| ||||| |||||||| ||||||||||| || ||||| ||||||||
gtcggtctccgcccgccgacgatcttcggctcccatctccctcgtcccgtatgttttcaggcaggatcattgctactgaacctgtcgtcgaaatctgactctgacctgtgggtccgtgctgctgccgccgccgccgctatatccgctcccccgtgcgtgatgcagGCGACGATCGGGATCGACTTCCTGTCCAAGACGATGTACCTCGAGGACCGCACCGTTCGCCTTCAGCTCTG
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
--------------------------------gtgcgtactctgc-gcatttcctttacaacgacaacgcctga-catgcttttgcggtctccg-tgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
|| || | | | | ||| | | || || || | |||| ||||||| || || |||||||| |||||||||||||| ||||||||||| || | |||||| | || || |||||
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 1
-------------------gtgcgtactctgcgcatttcctttacaacgacaacgcctgacatgctt--------------ttgcggtctccg---tgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
| ||| | | | || | |||| | | | | | ||| |||| | ||||||| || || |||||||| |||||||||||||| ||||||||||| || | |||||| | || || |||||
agtattattttgagttaatttatgtaatttttg-gcttgttgtacagtaatgctggttagtctattcaggtttgctcaaagttgttttctctggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------gtgcgtactctgcgcatttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
|| || || |||| || | | | | ||| || || |||||| || || || |||||||| || || |||||||||||||||||||| ||||||||||| || ||||||||
gtgaattaatttttaataactttcttctctgtgcaaatgtaactttgctgcaagctctgtatggtttcatgggctagtttctcagcgaatctagaggagagtcattagcggttttgagtccttcatgcatcatacttgttcttaatgctctgtttgtacttcattcgtttcg--gcagGCAACTATTGGAATTGACTTTCTCTCCAAGACCATGTACCTTGAGGATCGCACTGTGCGACTACAGCTCTG
upper sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------------------gtgcgtactctgcgcatttcctttac---aacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
|| | | || | || || || | || | | | ||| | || ||||| |||||||||||||| || || || |||||||||||||||||||| || || ||||| || ||||||||
gtgagattcttttttatcctctcatctgtgtataatagacttttactcgtaatccctgcagcttctgtgtgatttcattcaccatctttcaaagagatatagaaaatatacattggtaattttgagaatacactagacttgattttgaagaattaattatgtcttgtttgattcg-acagGCAACCATCGGTATTGATTTTCTCTCTAAGACCATGTACCTTGAGGATCGTACCGTGCGACTACAGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcgcatttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
gcctgac putative branch site (score: 3)
tctccgt putative PPT
tttacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtactctgcgcatttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC