Sequence
atgc intronic sequence ATGC exonic sequenceGTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg...
Basic information
| species | Physcomitrella patens |
| transcript | PP1S4_277V6.1 |
| intron # | 2 |
| splice site | 5' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagag--aagttc--tgctttgctaacaaggtgacctttgttg--
||||| ||||| ||||| ||||| |||||||| || | ||| ||||||||||| || || ||||| ||||| ||||| || |||||||| ||||| ||||| | ||| | ||| ||| || |||||| || | | || ||| | | | ||| | | ||| || | | || |
CTTGACTCATCCTGAGCTATATGAGGACATTGGAATAAGGCCTCCCAAGGGAGTAATATTATATGGGGAACCTGGCACAGGCAAAACTCTACTTGCAAAGgtttgtctctttttcttagga------cattgaagtcttgaattcccatgtttactccatttcaaattcaattcattaataaactagtaacttaataaatgctagt
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatac---gtttggcaaagggtgagatcatgtaattcttgact----tgcta-ccttgtctctgtacagagaagttctgctttgctaacaaggtg--acctttgttg------------------------------------------------------
||||| ||||| ||||| |||||||||||||| |||| ||| ||||||||||| || || || || ||||| || || ||||| || || ||||| ||||| | | | || || | | ||| || || | || | ||| | | | || | | || | | | ||| | | | |||
TTTGACCCATCCTGAGCTATATGAAGACATTGGCATCAGGCCACCCAAGGGAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatac---gtttggcaaa-gggtgagatc---atgtaattcttgac-ttgctaccttgtctctgtacagagaagttctgctttgctaa--caaggtgacctttgttg------------------------------------------------------------
||||| || || ||||||||||||||||||||||| | ||| ||||||||||| || || ||||| ||||| || || || |||||||||||||| ||||| | || || | |||| |||| || || | ||| |||| | | | || || || | | ||| | || | ||
CTTGACTCACCCTGAGCTGTATGAAGACATTGGTATTAGGCCTCCCAAGGGAGTCATATTATATGGAGAACCTGGAACAGGAAAAACTCTTCTTGCCAAGgtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggctttgatatctgcctttgtctatgtttatccaaattacactctttttctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg--------------------------------------------------------------------------------------------
||||| ||||| ||| |||||||||||||||| |||| ||| ||||||||||| || || ||||| ||||| || ||||| |||||||| || || ||||| | | | | ||| | || | || || | | | | || | | | | | | | | | | | | | |||||||
CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgc-tcaggctt---gcaagcatacaagatatctgtaatattgcttagtgt-tattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatac-gtttggcaaagggtgagatcatgtaattcttgacttgc-taccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg-------------------------------------------------------------------------------------
|| |||||||| ||||| ||||| |||||||| |||| ||| || ||||||||||| | ||||| ||||| || || ||||||||||| || || ||||| | | | || ||| || || || || | ||| | |||| | ||| || || | ||| | || ||
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg
|||||||||| || |||||||||||||||||||||||||| || |||||||||||||| ||||| ||||| || |||||||| || | ||||| ||||| | ||| | | | || ||| | | | | || | | ||| | | ||| || ||| | ||| ||
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgact-tgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg-
|||| ||||| || |||||||||||||||||||||||||| || |||||||| ||||| || || ||||| || |||||||| || | || |||||||| | ||| | | | || | || | | || | ||| | | || | || || | ||| || || ||||
CCTGACGCATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattttttggggtttcttatatggggcgatggaatataatcctgacatgttttt-tattcctcattttctctgt-ttaataacatggagtttgaaat
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgt----aaatacgtttgg-----caaagggtgagatcatgtaattcttg-acttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg-----------------------------
|||||||||| || || ||||||||||||||||||||||| || ||||| || ||||| ||||| ||||| || |||||||| || | ||||| ||||| | || |||| | | | || | || | || | | | || | | || || | | || |||| | |||| | |
CCTGACACATCCTGAACTATATGAAGACATTGGTATCAAGCCTCCTAAGGGGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatt-taaggagtgttccagcatcttaagacaatgccttttgtgtattcag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAG-
|||| ||||| || || ||||||||||||||||||||||| || ||||| || ||||| ||||| ||||| || |||||||| || | ||||| ||| || || ||| || | | | | | | | | || | | | || | || || | ||| | | ||||
CCTGACGCATCCTGAACTATATGAAGACATTGGTATCAAGCCTCCTAAGGGGGTCATTTTATATGGAGAACCTGGAACTGGGAAGACATTGCTTGCGAAGgtttgtgtttatcttttgcttcttctagagctgttttaatagagtttcaacatctcctttttactatctttatcttttggcagtgtttcaatttaaggagtgtttcagcatcttaagactatgccttttgtgtattcag
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttc--tgctttgctaacaaggtgacctttgttg
|| |||||||| |||||||||||||| ||||| || ||||| || || || || || ||||||||||| || ||||||||||| || | ||||||||||| | | ||| || | ||| ||| || | ||| ||| | | || | || | | || | | || || |||
TTTAACACATCCCGAGCTGTATGAAGATATTGGAATTAAGCCACCAAAAGGTGTGATCTTGTATGGTGAGCCAGGCACTGGGAAGACATTGCTTGCTAAGgttcgt-cttttagcctatagtgtatccattatataataagctttctagttgttaattgcttaatacagcacataatggtacttcccaagtatgattggtt-
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctc-tgtacagagaagttctgctttgctaacaaggtgacc-tttgttg
||||| ||||| ||| |||||||||| |||||||| || || || ||||| || |||||||||||||| || || |||||||| || | ||||||||||| | | | | | | | | | | || |||| | | | | ||| | | | | | || | | | |||||
TTTGACTCATCCTGAGTTGTATGAAGATATTGGTATTAAACCACCAAAGGGTGTAATTTTGTATGGTGAGCCTGGAACTGGGAAGACATTGCTTGCTAAGgtttgtctttgtacctagaatctaatgagtattagtgtttgtttgcagtatagcttagtttactacttaacttgtcaattacattcagttaatcgtttgt--
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatac----gtttggcaaagggtgagatcatgtaattc--ttgacttgctaccttgtctctgt-acagagaagttctgctttgctaacaaggtgacctttgttg
| |||||||| || |||||||| ||||||||||||||||| || ||||| || || | ||||| || || || || || || || | ||||| ||||| || |||| | | || | | | || | ||| | || | ||| | | | | | || ||| | | | || ||
TCTAACACATCCTGAACTGTATGAGGACATTGGTATCAAGCCTCCTAAGGGGGTCATACTATATGGAGAGCCTGGAACAGGAAAGACCTTGCTTGCAAAGgtgtgtattcatatttgcttcctatcaaactggtgcattacaatttatctgccattttatatctctgattgtgccatcctctttttcctt-----tcattttggt--
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtt-tggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg
| || |||||||||||||| || |||||||| ||||| || ||||||||||| || | ||||| ||||| || ||||| ||||| || || || ||||||||| | | | |||| | |||| || ||| ||| ||| ||| |
ACTTACGCATCCGGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaaatgtgacatctttgaaggtgctacttcgtaa---ttaactagct---ttggttctacag--------------------------------------
upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg
| || ||||| |||||||| || |||||||| ||||| || ||||||||||| || | ||||| ||||| || ||||| ||||| || || || ||||||| | || || | || | || ||| | ||| ||| ||| | | |||||
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtg----tgacatcttttaaggtgctgc--ttcgtaactaactagctt-tggttctacag------------------------------------Mapped 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|37841464|gb|BJ599472.1|BJ599472EST: CTGGGAAAACTCTTCTTGCTAAG GCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
genomic: CTGGGAAAACTCTTCTTGCTAAGgtaaatacgt ... tgcaatgcagGCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
EST:
gi|162171249|gb|FC346394.1|FC346394EST: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAG GCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
genomic: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgt ... tgcaatgcagGCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
EST:
gi|162224576|gb|FC400472.1|FC400472EST: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAG GCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
genomic: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgt ... tgcaatgcagGCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAG
EST:
gi|162216137|gb|FC392970.1|FC392970EST: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAN GCTGTTGCAAATTCCACGTCTG
genomic: GAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgt ... tgcaatgcagGCTGTTGCAAATTCCACGTCTG
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:
32 (upstream exon),
35 (downstream exon)
Score:
12GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgt ... tgcaatgcagGCTGTTGCAAATTCCACGTCTGCCACATTTCTTCGTGTTGTAGGAAGTGAGCTGATACAGAAGTATCTAGGAGATGGACCGAAGTTGGTGCGAGAGCTAT
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