Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgataatctctccaggtgactaagaaatttttgatcatattgcattggtatgtctgacgtgccgcgcgctatcttcgtttcaatctatcaaattgttatgttgaactttacgattggctgatcaatgttaattgtggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTCGACCAGACCATCTGGTCGGCTATTTGGAATAGTATCTACTTCATAACTC

Basic information

species Physcomitrella patens
transcript PP1S79_119V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_119V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G001724_T01 (Zea mays), 3'ss of exon 3
gtatgtgataatctctccaggtgactaagaaatttttgatcatattgcattggtatgtctgacgtgccgcgcgctatcttcgtttcaatctatcaaattgt-tatgttgaactttacgattggctgatcaatgttaattgtggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTCGACCAGACCATCTGGTCGGCTATTTGGAATAGTATCTACTTCATAACTC
                                               |||   ||||  | |  |          | |    ||  |  ||| ||   | | || |   ||| |   ||| |  | |  | | ||  || ||   |  |||    |||| || ||  | |  |||||||| ||||| |  || || |||||||| |||||||||||||| || || ||||| |||||||||||  |     
---------------------------------------------cacatatatatgaatcattttaattttttcaacaattttggaggctaacatgctttctaaggcaaacct---gatggagtaaatacttttg-ttatgt--tgacagGCACTGTTCCCATTCAAGGATTGGTGGGTTGTCCCTGCAAAGGTTGCATTCGATCAGACCATCTGGTCTGCGATCTGGAACAGTATCTACTTTGTGGTCT

upper sequence: PP1S79_119V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G03410.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgataatctctccaggtgactaagaaatttttgatcatattgcattggtatgtctgacgtgccgcgcgctatcttcgtttcaatctatcaaattgttatgttgaactttacgattggctgatcaatgttaattgtggaattgca---gTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTCGACCAGACCATCTGGTCGGCTATTTGGAATAGTATCTACTTCATAACTC
                                                                      |    |       ||   ||| ||||   | ||||||| | || || |  ||||||    |   |||  |    ||| |   |  | | ||||| ||||||| ||||||||||||||| |  ||||| ||||| || || ||| | ||||| || |||||||| ||||||||||| | |  | 
----------------------------------------------------------------------gtaaaaatcaatctttgctctgtcaa---gatatgttgta-ttaacaacgggctgaaagctaa-aatcttttctttgtacaagGCTCTCTTTCCTTTTCAAGAATGGTGGGTAGTCCCTGCAAAAGTCGCATTTGATCAAACCGTATGGTCTGCAATTTGGAACAGTATCTACTTTACAGTTT
















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|162264787|gb|FC440354.1|FC440354
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162187828|gb|FC364402.1|FC364402
EST:     GTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTC-AGNGATGGTGGGTAGTCCCAGTGAAAGTAGCATT
genomic: GTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAG-GATGGTGGGTAGTCCCAGTGAAAGTAGCATT
EST: gi|162183031|gb|FC360597.1|FC360597
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162192850|gb|FC369662.1|FC369662
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162246113|gb|FC421924.1|FC421924
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162192851|gb|FC369663.1|FC369663
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162273185|gb|FC449205.1|FC449205
EST:     GTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTCTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162273186|gb|FC449206.1|FC449206
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162251432|gb|FC425552.1|FC425552
EST:     CACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: CACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162196349|gb|FC373027.1|FC373027
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|162256233|gb|FC432289.1|FC432289
EST:     TACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: TACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
EST: gi|208365934|gb|DC955481.1|DC955481
EST:     GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAG                         TTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC
genomic: GATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTC

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: 35 (upstream exon), 35 (downstream exon)
Score: 42

ACCGGTTCTCGAGTTCAGCAGAGTCAGGCTTCTGAGATCAGGTCTTGTTGGATTTTGCCTTCACGGCTCTTTGTCACACTACTACTATCACGTTTGCGAGgtatgtgata ... ggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTCGACCAGACCATCTGGTCGGCTATTTGGAATAGTATCTACTTCATAACTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgttatgttgaactttacgattggctgatcaatgttaattgtggaattgcagTTTTTGTTTCCGTTTCAAGGATGGTGGGTAGTCCCAGTGAAAGTAGCATTCGACCAGACCATCTGGTCGGCTATTTGGAATAGTATCTACTTCATAACTC
                                   tgttaat  putative branch site (score: 42)
                                 aatgttaatt  TA-rich tract