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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat...

Basic information

species Physcomitrella patens
transcript PP1S97_167V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G016817_T02 (Zea mays), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGA-TAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattatttccaattga--aattactacat------
        || || ||| |  | ||||||||||| ||||| ||||||||| |||| |||||||| ||||| |  | ||| |||||||  |  ||   ||||| | | || |   | |  |   | ||   ||| |   ||   ||    | ||  | |   | | | |||  | | |  | |  | |||    |   ||||||      
------AGAAGGATTGGTTGGCGTTAGTTGCTGTCCACAGCGATGCCTGGTTACTAGCTGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaac--gattccaggcactggaacttttcagtttccttgaaaaagaaatttat-atatctattgttttgtgttctttatttgcctgaagcctacattttcac

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G04040.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtattt--ttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat----------------------------------------------------------
        ||||||||||| |||||||||||||| || |||||||| ||| |||||||| |||| |||||||  |||||      | ||||||||||    || |||| |    |    |||  | ||| | ||  ||     ||   ||   |||  |    ||  || | |  || |    |  ||  |   |  |   |   |||                                                          
------AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTACTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgtac--actgaacatacttcttatttgaagttaacttaagttggtggaaaatcacaaagcagttgaatcctgcttgtctgatttatccatctcattggtttagttcttttcttcacgtgtctcattcactcatgatttgaatatgtaatgcag

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G34250.1 (Glycine max), 5'ss of exon 1
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTG------ATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccac--acccattcatgtatt-atttccaattgaaattactacat
        || |||||||| ||||| |||||||||||||||||||| ||| | |||||||| ||||| ||||  || ||| ||||||      | |||   || ||||      | |    |  ||  |||  ||  | |   ||  | |  | |  | || | |     |   || |||| |||   |       || |||  ||   
-------AAAGGACTGGCTGTCTTTGGTTGCTGTGCACAGTGATGCTTGGTTGCTTGCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGACAGgtacctattttcctttctattcaata-tgtatatgggtttaactgattattattttttctcttaaatgatgcatgcatttgatcttgggcgatattgttaa--

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G00680.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctatc---------tgaacttgatataatgctgcttcttttttgt-----atttttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat---------------------------------------------
        ||||||||||| |||||||||||||| || |||||||| ||| | |||||| |||| |||||||  |||||      | ||||||||||    || |||| |   ||          | ||  | || | | | |   |    || ||     ||     |  ||||    |   |   |     |  | | ||  ||||   ||||| | |                                             
------AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTGCTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcatactctgaccataaatcttatctgaagttaacttaagttggtggaaaatcacaaagcagttggatcctgcttgtctgatttatgtatctcattggt-ttacttcttttcttcacgtgtctcattctctcttgatttgaatatgtaatgcag

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA09G07970.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgcca--cacccattcatgtattatttccaattgaaattactacat--
        || |||||||| |||||||||||||| ||||||||||| |||||||   | || |||||||| |  || ||      | | ||||||||    || |||| |  ||  |    ||  |  ||| ||  |  | | || || | |    || || |  ||      || | |     | |||  |||  |    | | | |  
------AAAAGGACTGGCTATCTTTAGTTGCTGTACACAGTGATGCATGGCTACAATCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagttc--ttttctccaatcct-ttattatcttatactctctg-gaattgtttcaggtgttcaatgagaacatgttttgaatgcatgccattgccttt

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA14G11400.3 (Glycine max), 5'ss of exon 2
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTG------ATAAGAACGAGAGgtc--tgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattat--ttccaattgaaattactacat
        || |||||||| ||||| |||||||| ||||||||||| ||| | |||||||| ||||| ||||  || ||| ||||||      | |||   || ||||   |  | |||   ||    |  |||    |    ||   |  || | |    || |   | |   || |||||||| |  ||       | |||  ||   
------AAAAGGACTGGCTGTCTTTGGTTGCTGTACACAGTGATGCTTGGTTGCTTGCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattttcttttctcttcaatatgtatatggacttagctgattattattttttctctta-agtgatgcatgtattttgattttgggcaatattgtta---

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G16740.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat-------
       ||| |||||||| ||||| ||||| || ||||||||||| ||| ||||||| || |||||||| |  || || || |||| |    |  | || |      | |||   || | |    ||  || || | | | ||| |  | | | ||  |         || | |   ||| |   ||   ||  |   |       
------ATAAGGACTGGCTGTCTTTGGTTGCCGTTCACAGTGATGCATGGTTACTTGCAGTGGCTTTCTACTTTGGGGCACGATTTGGTTTTGATAA-AGCTGACAGgtatgattctgttttctaactctttattgtgtttttttcttgcaattgatctctaggttggacagggaaatttttcggatgcctttcgtttttcatttac

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G26210.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTT------TGATAAGAACGAGAGgtctgc-tatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattatttccaattgaaat--tactacat--------------------------------------------------
        || || ||| | ||  | |||||||| ||||||||||| ||||| |||||||||||||||| ||  |||||  ||||      ||| ||    || |||| ||  ||||         | |||  ||  |   || ||  || | ||     |  ||  | |   || || |  |      || |     |  |||| | |                                                  
------AAAAGGATTGGTTGTCCCTTGTTGCTGTCCACAGTGATGCTTGGCTTCTTGCTGTTGCTTTCTTTTTTGGAGCCAGGTTTGGATTTGACAAAGCTGATAGgtatgtatatccttctcctctttaagtctaatc--ttcttacatctatgttccttggtggtatatagatgcaagcctctcagtcactcattgttctactccttcaccgtttatgtagctctctgtgatttatgttctttcacatttgttacag

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G20510.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGG-----AGCTCGGTTT-GATAAGAACGAGAGgtc---tgctatctgaacttgatataatgctgcttctttt----ttgtattt-ttgacgagt-tatgccacacccattcatgtattatttccaattgaaattactacat-----------------------------------
        | | ||||||||||| | |||||||| ||||||||||| ||| ||||| ||||  |||| || |  ||        | ||||| ||||     || ||||    | || |||    | | |    || |   |||| |    | || ||  |||   | | | | |    | || |  | ||  |||    ||    ||  ||  |                                    
------AAAGAAACTGGCTTTCTCTCGTTGCTGTCCACAGTGATGCGTGGTTACTTTCTGTGTCTTTTTACTTTGGTTCAAGATTTGGTTTCGATAGAGCTGACAGgtatcattctttctttcttggttgctgtgttttctcttctaacctggtgttcgttgtttaatatcttctctgctcaattctctaccattaattatcatgatatctgaagcatttccatactaacccgtacacttacaaattcag

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv09s0002g01600.t01 (Vitis vinifera), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtatt---atttccaatt--gaaattactacat---------
        ||||||||| | |||||||||||||| || |||||||| ||| | ||||||||||| |||||||  || ||  | ||||        || |   |||  |       ||   ||    |   ||||||||  |   || ||     | |||  ||    || | || ||     ||  |||   |||   |   |||         
------AAAAAGACTGGTTATCTTTAGTTGCTGTCCATAGTGATGCATGGTTGCTTGCTGTTGCCTTCTATTTTGGTGCCAGATTTGG---ATTTGATAAAGCTGACA----Ggtttttcatttctccttttctttttctttccttcgatataat-tgctgcaagagtttaggtttttaaggttttaatgaagaagggatagcatgggaacaaa

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv11s0016g01500.t01 (Vitis vinifera), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAA-GAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagtta-tgccacacccat-tcatgtattatttccaattgaaattactacat---
        || |||||| | ||| | |||||||||||||||||||| ||| |||||||||| || |||||||  || ||  |||||| |   ||   ||  | | | ||| |     |   | | |    | ||| |  |  |    | |    | | |  ||         ||   | |  | |||| |       ||  ||   
------AAAAGGACTGGTTGTCTCTGGTTGCTGTGCACAGTGATGCTTGGTTACTTGCTGTGGCCTTCTATTTTGGTGCCAGGTTTGGTTTTGATAAAGCTGACAGgtatatctttctttaacattctaacctctgtcctagaggcctaattcctgagtttcatctttgcaccaaaaacttctcccaactttttcgccttgatcgt

upper sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAG-
        ||||||||| | ||  | |||||||||||||||||| | ||| | ||||||||||| |||||||  || || || ||||         |||| |   | || |     |||  |     |||   ||||  ||| ||| | |   || |     ||    ||  | | | | |     |  |||| |  || ||     
------AGAAAGACTGGTTATCACTGGTTGCTGTGCACAGTGATTCATGGTTGCTTGCTGTTGCATTCTATTTTGGTGCCCGCTTTGGGTTTGGTAAGAGTGAAAGgtaacactttttggaacttcactgaaactttcctgtctttctca-atgtcaaatttcaaatgtttttttgtgagtcatggtggtgaagtatctccagttct

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|67723789|gb|BJ974048.1|BJ974048
EST:     CTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAG                         AAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
genomic: CTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
EST: gi|100354113|gb|BY945717.1|BY945717
EST:     ACTTTGCTGT-GCTTTCTATTACGGAGCTNCGGTTTGATA-GAACGAGAG                         NAAGCGTCTTTTCACCATGATAAATGAGCTCCCAACTGTATT
genomic: ACTT-GCTGTTGCTTTCTATTACGGAGCT-CGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATT
EST: gi|18335857|gb|BJ167878.1|BJ167878
EST:     CTACTTGCTGTTGCTTTCTATTACGNAGCTCGGTTTGATAAGAACGAGAG                         AAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
genomic: CTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
EST: gi|18338539|gb|BJ170563.1|BJ170563
EST:     ACTTGCTGTTGCTTTCTATTACGNAGCTCGGTTTGATAAGAACGAGAG                         AAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
genomic: ACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
EST: gi|208373173|gb|DC945141.1|DC945141
EST:     CTACTTGCTGTTGCTTTNTATTACGGAGCTCGGTTTGATAAGAACGAGAG                         AAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT
genomic: CTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGT

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-Seq library.


Block sizes: 33 (upstream exon), 31 (downstream exon)
Score: 4

TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatc ... atatttacagAAAGCGTCTTTTTACCATGATAAATGAGCTCCCAACTGTATTTGACGTAGTCACGGGGAAAAAGCCTGTGAAGGAAAAGCCCGCTGTCAATAGCTCTGGC





























Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtatttttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC