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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgttacctgcctgtcttttatccttctgttctcaacgtgcctgtttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC

Basic information

species Selaginella moellendorffii
transcript EFJ33415
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33415 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctg------ttctcaacgtgcctgtttgtt-tgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC
                                                                                          ||  || ||  |   |  |||      ||| |      || | |       ||| ||   ||||||| ||  | |  |  ||||| || || ||||| |  |||||| ||||| |||||||||||||||| |||||||||||  |||| || || ||||| || |
gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC

upper sequence: EFJ33415 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctgttctcaacgtgcctg-tttgttt--------gcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC
                                                                                                                                     || |||| |    ||||   |   | ||||| |||  | |    || || |  |        |||| | || |  |  |  ||||| || || |||||||  ||  |  ||||| |||||||||||||||| ||||| || ||||| || ||||||||||| || |
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
















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|169018854|gb|FE427039.1|FE427039
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169075702|gb|FE481776.1|FE481776
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169115215|gb|FE516970.1|FE516970
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169029206|gb|FE439711.1|FE439711
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169024527|gb|FE436285.1|FE436285
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169025118|gb|FE434705.1|FE434705
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169041649|gb|FE448232.1|FE448232
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169088824|gb|FE494388.1|FE494388
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169031680|gb|FE437481.1|FE437481
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169029116|gb|FE439374.1|FE439374
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169051181|gb|FE458702.1|FE458702
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169087552|gb|FE494643.1|FE494643
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169095949|gb|FE497301.1|FE497301
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA
EST: gi|169031898|gb|FE440650.1|FE440650
EST:     AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAG                         GAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCA
genomic: AAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCA

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), 34 (downstream exon)
Score: 61

TTGTAACCCCGAAGGCAAACAGTTCGTTGAATCTTCAAAGACACCACAAGAAGTTGAAGTCGGGGAAGAGATCGTTTTCACTTACGACGTCAAATTCGAGgtaactgtta ... ttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttacctgcctgtcttttatccttctgttctcaacgtgcctgtttgtttgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC
                                        cctgttt  CT-rich tract
              tcttttat  TA-rich tract