Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S35_94V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
-gtaagaaactatcatcgt--------tgatactttagatgctttcaaatcttgtattgccgcg-ataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
| | | | | || || | || || | || ||| ||| ||| | | ||||||| | | ||| | || |||| || || || || || ||||| ||||| |||| || |||| |||| |||||||| ||||||| ||||||||||||||||| ||||||||||||||
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactgg-atg-attatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
-------------gtaagaaactatcatcgttgatactttagatgct-ttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
|| | |||| || | | || | || | ||| ||| || | | | | || || || ||| | | |||| || || || || || ||||| ||||| | || || |||| | || || ||||| ||||||| ||||||||||||||||| ||||| ||||||||
ccttatcatatatgttgcatacta-cagcttaaatgcatttgttgccattcctatttcattctagcatccctttaa--aagcttgcaccat---ggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
|| | | ||| |||| || | | | | ||| | | | | ||| | | | ||| ||||||||| ||| |||| ||||||||||| ||||| | |||| | || || ||||| | ||||| ||||||||||| ||||||||||||||||||||
-----gtacgtttcttgttttggacgtagagttgttaagggagcatgcagacttgattattccttgaatgtttacattttggcgctgc--agGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------gtaagaaactatcatcgt-tgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgct-cagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
| |||| | | | | | | | | ||| |||| || | || | | || || |||||| | |||| |||||||||| || |||| ||||| ||||| ||||| |||||| |||| |||||||| | || || ||||||||||| || |||||||||||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattc--ctcatattttg--tgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
----------gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggag-gatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
|| | || | ||| | | || | |||| || || | | | | | | ||| || | | || |||| ||||| || | || || || |||||| | || ||||||| |||| || ||||| | ||||| ||||||||||| ||||||||||| ||||||||
ttccttgtattccagttatctgcaaaatctataatatgaat-ttgtcaatcttttggtttttgtgttcaaag--atttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
||||| | || | | | |||| | | | | | ||| | || | |||||| ||||| || |||||||| ||||| || |||||||| || ||||| || || ||||| | |||||||||||||| |||||||| | || ||||||||
---------------------------gtgagcttttcactcctttttaagatcgatcactaaacgaatttattactt--gactacactcagGCAAGACCGTTTTCACGAGCGACCACGCTTTGAAGCTCGAATGGATACCAGATTGGATTGCCATTGTCGGAAGTGGCTACATTGGCTTGGAATTCAGTGA
upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
| | ||||| ||| || || | || ||| | | | | || | |||||| ||||| || |||||||| ||||| || |||||||| || ||||| || || ||||| | |||||||||||||| |||||||| | || ||||||||
-------------------------gtgagcg-tttcactccttttaagatcg-atcactaaacgaatttattac---ttgactacactcagGCAAGACCGTTTTCACGAGCGACCACGCTTTGAAGCTCGAATGGATACCAGATTGGATTGCCATTGTCGGAAGTGGCTACATTGGCTTGGAATTCAGTGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162195483|gb|FC370900.1|FC370900EST: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATG GAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
genomic: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
EST:
gi|162167619|gb|FC343751.1|FC343751EST: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATG GAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
genomic: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
EST:
gi|162166909|gb|FC343294.1|FC343294EST: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATG GAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
genomic: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
EST:
gi|162170369|gb|FC346774.1|FC346774EST: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATG GAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
genomic: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
EST:
gi|162189578|gb|FC365800.1|FC365800EST: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATG GAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
genomic: CATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
13 (upstream exon),
23 (downstream exon)
Score:
1TATGGAAAAATTGGATTTTCTGACAAAACTGTGACAGCACGCAACATTATCATTGCAACTGGTTCGGTGCCTTTTGTTCCTCCAGGAATTGAAGTTGATGgtaagaaact ... ggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA
atctgat putative branch site (score: 1)
aacaaaat TA-rich tract