Sequence
atgc intronic sequence ATGC exonic sequencegtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
Basic information
species | Physcomitrella patens |
transcript | PP1S15_262V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 3'ss of exon 5
gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgc-ttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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--------------------------------------------------------------------------------------------tcgatgatttattaatgatcaagttgcttttaccagactttgattttgtcaatga-gcatactcaataagttaattcggttttg------ttttgcaatatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCTCTGTGTCTCCGTACTATGGAGATGGGCAGTGAACTTTCGAAAACG
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 5
gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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----------------------------------------------------------------------------------------------attgt-ttcttgaattttttttttttgtaattcatatttcatctattcttgtttttttatcaattgtgacattttttttctgtctgatttttattcac---tagGTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCCCTGTGCCTGCGCACCATGGAAATGGGCAGTGAACTATCCAAAACA
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G10400.1 (Glycine max), 3'ss of exon 5
gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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-------------------------------------------------------------------------------attatcattgtttttaaatttttttttgtaatccctatttc-------atct--attcttttgt-----ttttgttaattctgacatttt-tcctggctgatttttattc-ac---cagGTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCTCTATGCTTGCGAACCATGGAAATGGGCAGTGAGCTATCCAAAACA
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 5
gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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-----------------------------------------------------------------------ctagtgggatgaagctattgttttttttgttgcttg---tcacatgtacaattatactt-gagttttgtcgtgtttaattt------------attttctgttga--------tatttcac---cagGTTGATGATACAGAGGTTATAAGTTTCCTTCTTTCAACAGAGATTATTCCGCTGTGCCTGCGCAGTATGGAAATGGGCAGTGAATTGTCAAAAACT
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccg-agataattcggaatttgttgtagatgtttttata----atgaagagattttatattaacgggactctgttctacatac-agGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
||| | || || | || || | | | |||| | || | ||| | || ||| | || | ||| | | | | | || | ||| |||| | | | || | | ||| | || || | | || || | | | | | | | | |||| ||||| || || || |||| || || || ||||| || |||||||||||||| || || || ||||||||||||||||| || || || ||
gtacaccatcccgtcccttttctgttccttgtttctc---tttggttttgatgttccccacctactttttgctga--aagcaaaggactaaaaatt-----gtgttagtggtcttggtttctaaagtagagaatttatattcttttttggtggttagtgtatgaaataagaaaggttcatcggatccttatttcactttgttttccagGTTGATGATACAGAGGTCATTAGCTTCCTTCTTTCAACTGAAATTATTCCTCTGTGCCTCCGTACCATGGAAATGGGGAGTGAGCTGTCAAAAACA
upper sequence: PP1S15_262V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 7
gtgatcacttctattgccagtcgctcagaaccggagtggaagctgaatgtgcaggccccgtatcggtctgcccagtcagtttacttatttttttagtgcattatttgacatcgcttgctccgagataattcggaatttgttgtagatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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---------------------------------------------------------------------------------------attaattgctatattgtttg-tattgtttgt------aaggtttg----ttactcttgtgattccaagtattgctggttattaccttttttattttttcccctctttccagGTTGATGATACAGAAGTTATTAGTTTCCTTCTCTCAACAGAAATAATTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACAMapped 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|18356452|gb|BJ188511.1|BJ188511EST: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAG GTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAG
genomic: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAGgtgatcactt ... ctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAG
EST:
gi|208348349|gb|DC905549.1|DC905549EST: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAG GTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCT
genomic: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAGgtgatcactt ... ctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCT
EST:
gi|100356823|gb|BY965298.1|BY965298EST: TCGAGTATCTTCGATTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAG GTGGATGACACTGAAGTTATTTATTTTCTACTCTCAACAGAGATTATTCCT
genomic: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAGgtgatcactt ... ctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCT
EST:
gi|100368244|gb|BY948190.1|BY948190EST: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAG GTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCT
genomic: TCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAGgtgatcactt ... ctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCT
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:
9 (upstream exon),
32 (downstream exon)
Score:
2TCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAAGACCGTTCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCTTGTTAAGgtgatcactt ... ctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatgtttttataatgaagagattttatattaacgggactctgttctacatacagGTGGATGACACTGAAGTTATTAATTTTCTACTCTCAACAGAGATTATTCCTCTGTGTCTACGAACTATGGAAATGGGGAGTGAACTTTCCAAGACC
tattaac putative branch site (score: 2)
ctctgttct putative PPT
tttttataatgaagag TA-rich tract