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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcccaattttgtggcttaattaattatgaacacattacaaacttatttgggcctaaaagtttgttaatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG

Basic information

species Glycine max
transcript GLYMA17G11800.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11800.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g55220.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------gtattcccaattttgtggcttaattaattatgaac---acattaca---aacttatttgggcctaaaagtttgttaatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG
                                       | |  | |||   |      |  | |||| |     ||  || |   ||| || |||  ||||  |  |   | |   | ||||||||||  || ||||||||||| |||||||| ||||| ||||| |||||||| || ||||| |||||||||||||| ||  | ||||| |  || || |
gtaatttattcatcatatatggacaaactactggtcacaaataaccattacatactcctaacagttattagtattacgctatatttaacataattgctcctatcatgtgtctgac--cgcagGTTGTGAGCGAAAGCTTGAATCCAGTTTGGAACCAAACTTTTGATTTTGTTGTCGAAGATGGTTTACATGATATGCTTATGTTGGAAGTATATGATCATG

upper sequence: GLYMA17G11800.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G071163_T01 (Zea mays), 3'ss of exon 11
----------------------gtattcccaattttgtggcttaattaattatgaacacattacaaactt-atttgggcctaaaagtttgttaatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG
                        |   |||   |  ||   |  | |   ||         | |  ||| |  ||  ||||  |  |   | |   | ||||||||||  || |||||||| || || ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||  | ||||| |  || || |
ttctatttatattcggatcagtagagaaccataataatgctatggtcagaaattgcttgggcaaagtcttcaactgtccctatgatgtgactgac--cacagGTTGTGACCGAAAGCTTGAACCCAGTATGGAATCAAACTTTTGATTTTGTCGTTGAAGATGGCTTACATGACATGCTTATGTTGGAAGTATATGATCATG

upper sequence: GLYMA17G11800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G05500.1 (Arabidopsis thaliana), 3'ss of exon 11
----------gtattcccaattttgtggcttaattaattatgaacacattacaaacttatttgggcctaaaagtttgttaatttc-tcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG
            |||   |   |    |  | ||  ||  |  | |  || ||  ||  |      ||||  |    ||   |||  ||||| || |||||||||||||| || || ||||| || || ||||| ||||| ||||| || || ||||||||||||||| |  ||||||| ||||||||||
gtaagtcctctcatttaaagcatcaaagagttatccatgttatagatgtttcatcctcctcattaactaatggcaattttgcttcaccagGTCGTCAATGACAGCTTGAACCCGGTATGGAACCAGACTTTTGATTTTGTAGTTGAAGACGGGTTACATGATATGCTAGTCCTTGAAGTCTGGGACCACG

upper sequence: GLYMA17G11800.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0118g00230.t01 (Vitis vinifera), 3'ss of exon 10
---------------gtattcccaattttgtggcttaattaatt---atgaacacattacaaacttatttgggcctaaaagtttgttaat---ttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG
                 ||||  |  | ||    | | ||  |    ||   || ||||     | | ||     | |   ||  ||  |   |||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||| ||| | ||||| |||||||| |
atgttctgtgtcccgaaattcttacatgtggaagtaactttctctaaatatgcagattatgggttgacttaattttcagcattcttttttgtgttctcagGTTGTGAATGATAGCTTGAATCCAGTTTGGAATCAAACTTTTGACTTTGTTGTTGAGGATGGATTGCATGATATGCTGATTCTGGAAGTCTGGGACCATG

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|6913840|gb|AW395370.1|AW395370
EST:     AAACAAAACCAGG                         GTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT
genomic: AAACAAAACCAGGgtattcccaa ... aatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT
EST: gi|20813758|gb|BQ298236.1|BQ298236
EST:     CTTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACCAGG                         GTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT
genomic: CTTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACCAGGgtattcccaa ... aatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT
EST: gi|11412226|gb|BF424237.1|BF424237
EST:     TTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACCCAGG                         -TTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGG
genomic: TTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACC-AGGgtattcccaa ... aatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGT
EST: gi|254342026|gb|GR853163.1|GR853163
EST:     CTTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACCAGG                         GTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT
genomic: CTTTTGTTGTTCTTACCTTGAAGAAAGCAGAAACAAAAAACAAAACCAGGgtattcccaa ... aatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattatgaacacattacaaacttatttgggcctaaaagtttgttaatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG
                                         tgttaat  putative branch site (score: 3)
                                               tttctc  CT-rich tract
                                 taaaagtttgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcccaattttgtggcttaattaattatgaacacattacaaacttatttgggcctaaaagtttgttaatttctcagGTTGTGAATGACAGCTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG