Sequence
atgc intronic sequence ATGC exonic sequencegttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S122_29V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
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-------------------------------------------------------------------------------------ttatactttatatttcgtgggcatgataccttgtacctgtactg----ataatttatatcttttgtactaatagaagtgtcttggtgctt---gttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
---gttgaacttttaatcatgt---tttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacc-cttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccg-gctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
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gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaat--cttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacc--tgtactgataatttatatcttttgtactaatagcagtgtctttgtgcat---gttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgcc-ggctatttctt--ctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
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----------------------gtaagggcgccat-gta-ttattctctgagatcatta--tatgaatctagtacaaatattaagcttggt---agttatttgtggattaggtgaatggaaaatctatatttggtt-cttatcattttcccagttaataactaacatattatgttccactgttgccttga-gtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
|| | | | ||||||| || | || |||| ||| | | | || | | || || | || | ||| |||| | | ||| |||||| ||| ||| | ||||||||||||||||| || |||||||| || || ||||||||||| ||| | || || ||||| |||||||| |
--------------------------------------------------------------------------------ttgagtgaaaaaa-ggttaccttctaggtgtcatcaag-atca----tgtcccctttcttattgctagttggtgatctagtcctttt-tgtgttttgtctctg-----gcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ32651 (Selaginella moellendorffii), 3'ss of exon 18
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtg-attacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
||| | |||| | | | | ||| | || | || ||||||||| || || || |||||| ||| |||||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||||||| |
------------------------------------------------------------------------------------------------------------------------------------------gtacgatttgccaatg------cccgtgtgcatgcttcaaactagagtgttccagGTACTGCCGTTGCAACCCGGGGCTCTTCAAATCTGCCGACACAGCTTATGTTCTGGCATATGCAGTTATTATGCTCAACACGGATGCCCATAATCCTATG
upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ20775 (Selaginella moellendorffii), 3'ss of exon 17
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtg-attacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
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------------------------------------------------------------------------------------------------------------------------------------------gtacgatttgtcaatg------cccgtgtgcatgcttcaaactagagtgttccagGTACTGCCGTTGCAACCCGGGGCTCTTCAAATCTGCCGACACAGCTTATGTTCTGGCATACGCAGTTATTATGCTCAACACGGATGCCCATAATCCTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
ttctgac putative branch site (score: 2)
tatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG