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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG

Basic information

species Physcomitrella patens
transcript PP1S58_256V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
| || ||| | | | || ||| || | |||| ||| | |||| |||| || |||| ||||| || | || ||| |||| || || || || | |||||||||||||| || ||||| |||||||||||||||
-------------------------------------------------gtaagttcaagctgcactataatcatggcacacagttacatctactataaccacca-tagtgttgtcttcgcatctacataat-----------gtctaacaagttc---atcctc------agGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G014116_T02 (Zea mays), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggta-tgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
| ||| ||| ||| || | || | |||| | | || | | | || ||| | || | | || ||| || | ||| || | |||| || |||| || || | || ||| || || || || ||||||||||||| |||||||||||||||||||| ||||||
----------------gtaagtttgccccgcact-ataattgaggacatgtaattccatattctgtgacaatgtttttgtcattctttagtaccgttcctcaattctca-------ctatccatgactataatgga----------ctaacaa----gctgtttatca-----gGTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G013750_T04 (Zea mays), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaac-cagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatga--agGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
| || | || | | | | || | ||| || ||| | | || || | || | | | || | | || | | | | | |||| || || || || | ||||||||||| |||||||||||||||||||| ||||||
-------------------------------------------------------------------------tgaaccctaaatactacggtattcataaattccatagttttatct-tgaaactccaaaaatactgagct--accaaaacaggccctaacaagctatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaa-gtggtatgcggtgcctgaaccagtaga--ttggtctacgcagctttctaattgatgcacctgatctaataatgttgcaa-tactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
||| ||||||| ||| | | | | | ||| | ||| | | | | | |||||| | | | || | ||| || || | ||||||| || |||||||| ||||| ||||| ||||||||||| |||||||| || ||
------------------------------------------------------------------------gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagt--attcagtttacttatggaatgggtaatctga-acagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
| | | | | | | | | | | || | || | ||| || || || | || | || || || | | | |||||||||| || |||||||||||||| || |||||||||||||||||||| || ||
-------------------------------------------------------------------gtaagcttttcttcctctactttccaactttcgtggaaatcgttt--tttattta-ttttatagtttatcaatgtgcattgat-----tgtgattatgaattatagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAA

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
|| || |||| | | | | | || | || | | | ||| | ||| | || || |||||||||| || |||||||||||||| || ||||||||||| || || || || ||
-----------------------------------------------------------------------------------gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacc----cctgcaatttgataaataattaac--agGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA

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|162156858|gb|FC332804.1|FC332804
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|100438193|gb|BY961700.1|BY961700
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|208367351|gb|DC939867.1|DC939867
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|208350568|gb|DC910373.1|DC910373
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|208363544|gb|DC939749.1|DC939749
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|100418836|gb|BY975763.1|BY975763
EST:     AAGAACAGGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|100385804|gb|BY950998.1|BY950998
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|162225703|gb|FC401845.1|FC401845
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|162269559|gb|FC445115.1|FC445115
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
EST: gi|18344483|gb|BJ176523.1|BJ176523
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATT
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATT
EST: gi|100416003|gb|BY957030.1|BY957030
EST:     AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCA                         GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA
genomic: AAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTA

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: 30 (upstream exon), 35 (downstream exon)
Score: 25

TGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATCCGTGAAGAACAAGGGCAAATTGCTGAAGCCGCAGAATGCATGCAAGAAGTTGCAgtatgatccc ... tccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG
                         atctaataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG