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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGTGGAGCACGAGAAACCCGCTCGAATGTCCGTGGATGCCAACGACCTCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccattcagcttaactctagtttgaaagcgatttgcgtttctcaacctaaactgtactgctctattcagtcacatgtttttagacgaattttgat...

Basic information

species Physcomitrella patens
transcript PP1S6_67V6.2
intron # 3
splice site 5'
intron type U2

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|37822190|gb|BJ580256.1|BJ580256
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|37821746|gb|BJ579812.1|BJ579812
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCNTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208400020|gb|DC925246.1|DC925246
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208353328|gb|DC922466.1|DC922466
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162165245|gb|FC341708.1|FC341708
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|67695157|gb|BJ955390.1|BJ955390
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208368745|gb|DC955188.1|DC955188
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162234586|gb|FC410852.1|FC410852
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208375500|gb|DC945087.1|DC945087
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208363390|gb|DC946988.1|DC946988
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162173418|gb|FC349797.1|FC349797
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|37845409|gb|BJ603417.1|BJ603417
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|37842306|gb|BJ600314.1|BJ600314
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162233339|gb|FC410175.1|FC410175
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162237436|gb|FC412739.1|FC412739
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162202345|gb|FC378664.1|FC378664
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGGCCA-CAGCACCCCCTGAGAAA-G
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGG-CCAACAGCACCCCCTGAGAAAAG
EST: gi|162152981|gb|FC329283.1|FC329283
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208389485|gb|DC942192.1|DC942192
EST:     TCCCTCAATNAGCTGCTCGAAA-CTTGGTGCCGAGACCA-CACTCG-AAA                         GTTGTATTGGATGTTG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTG
EST: gi|37831473|gb|BJ589485.1|BJ589485
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208388717|gb|DC953465.1|DC953465
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|162224518|gb|FC399894.1|FC399894
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208397013|gb|DC924691.1|DC924691
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208350945|gb|DC917718.1|DC917718
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208358430|gb|DC930562.1|DC930562
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGNAAA                         GT-GTATTGGATGTTGGATT-GGCGGNC-ANCAGCACCC
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCC
EST: gi|208373197|gb|DC945151.1|DC945151
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|208373305|gb|DC948579.1|DC948579
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|37827512|gb|BJ585524.1|BJ585524
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAA                         GTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGG
EST: gi|100395067|gb|BY953590.1|BY953590
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCNACACTCGGAAA                         A
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcag-
EST: gi|100395067|gb|BY953590.1|BY953590
EST:     TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCNACACTCGGAAA                         A
genomic: TCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcag-

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: 28 (upstream exon), 8 (downstream exon)
Score: 1

TCATGTGGAGCACGAGAAACCCGCTCGAATGTCCGTGGATGCCAACGACCTCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccat ... tgatgggcagGTTGTATTGGATGTTGGATTTGGCGGGCCAACAGCACCCCCTGAGAAAAGGTGGCACAAGCCAGCGCAATGGTCAGACATTGAGAAGATTTTAGAAAAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGTGGAGCACGAGAAACCCGCTCGAATGTCCGTGGATGCCAACGACCTCCCTCAATTAGCTGCTCGAAAACTTGGTGCCGAGACCAACACTCGGAAAgtatgtccattcagcttaactctagtttgaaagcgatttgcgtttctcaacctaaactgtactgctctattcagtcacatgtttttagacgaattttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT