Sequence
atgc intronic sequence ATGC exonic sequencegtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
Basic information
species | Physcomitrella patens |
transcript | PP1S438_26V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
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--------------------------------gtaagaactcagtttc---tgcaattaaagcctggttctgcaccttggttcttatgtattttgttgccaattttccacataaaaaattatgccttgattctcaa-tttcccatgtatatcttgcagcatttcctctgaccacagataatccattttatggcagATCCATTGGTTCTCAATCTTCAATTCTTTCATGATGGTTATCTTTCTCACTGGGCTAGTGTCAATGATTTTGATGCGCACTCTAAGAAATGACTATGCAA
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatt-tgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccg-cgatga-cagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
| | | || ||| ||| | | | | | | |||| | || |||| | | || | |||| ||| || | |||| | | | | || | | || | | ||| | || || | ||| ||||| ||||||||||| |||||||| |||||||||||||| || || |||| || ||||||| ||||| ||||| | || || | || ||||||||||
--------------gtaatctttgttcgaac--caacattactttttatgtcttttgctggaca----gtttttgtgctataatttactttgctctgtggtggtt-ttgacaaagtggtagactttattttctttaaaactctcgaggaattgaaatttacaagaaaactaagttctgctgcaaccttccatgttcagATCCATTGGTTCTCCATCTTCAATTCGTTCATGATGGTTATTTTCTTGACTGGATTGGTATCAATGATATTGATGAGGACGCTGAGAAATGATTATGCGA
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacga-gtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatg------ttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
| | || |||| | | || || | | | | || ||| | || || || | | | | ||||| || |||||||| ||||| ||||||||||||||||| || || || || || |||| || ||||| ||||| | || ||| | || ||||||||||
------------------------------------------------------------------------------------------------------ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
|| | | ||| | ||| ||| ||| | | | | || ||| || || | | || | | | || ||||| ||||||||||| |||||||| || ||||||||||| || || || || || |||| || ||||| | ||||| || || || || |||||||| |
-------------------------------------------------------------------------------------------tgctagga-ggaattccatta-atgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaact-tggtg-cagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatg-acagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
||||| || || || |||| | | | | | || | | ||||| || ||||| || |||||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||| | || || || || ||||| |
----------------------------------------------------------------------------------------------------------------------------------------gtttgttgt-tgtctgtctttgtacaagtttaaactcctgcttgtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCCA
upper sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 6
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
| ||| | ||| || ||| || | || | | ||| | || ||||| || ||||| || |||||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||| | || || || || |||||||
------------------------------------------------------------------------------------------------------------------------------------gtttgtt-gtcgtctgtctttgtacaagtttaaactcctgcttg-tggtatcttcg--tgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGAMapped 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|162185785|gb|FC362341.1|FC362341EST: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAG ATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
genomic: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAGgtgggtgtga ... gcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
EST:
gi|162179317|gb|FC356266.1|FC356266EST: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAG ATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
genomic: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAGgtgggtgtga ... gcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
EST:
gi|67716951|gb|BJ967210.1|BJ967210EST: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAG ATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
genomic: TCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAGgtgggtgtga ... gcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACG
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:
34 (upstream exon),
33 (downstream exon)
Score:
19AAAGATCGACCTGACGTACGCAGTGCAGTGGGTGGAGACCAACATATCGTTCATCCGACGATTCGACGCGTACCTGGATTACCCGTTCTTTGAGCACCAGgtgggtgtga ... gcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA
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