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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaaactctatcctttattgtctttgagaatcatctgtttagcaacactttcagtattgtttaaagtttccttctttctctcttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATGGGGTGGAGTTCACTGTGGAAGAGG

Basic information

species Glycine max
transcript GLYMA05G28260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G336858_T01 (Zea mays), 3'ss of exon 1
gtacgaaactctatcctttattgtctttgagaatcatctgtttagcaacactttcagtattgtttaaagtttccttctttctctcttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATGGGGTGGAGTTCACTGTGGAAGAGG
||||   ||  ||| ||    |||  ||      ||  |   |           ||  ||| || || | |  ||   |      ||||  |||||||||| |||||| |||||||| || || |||||  | || ||||||||||| || ||||||||||||  ||| |
gtactgtaccatattctactctgttgttcgattccacgttgctgtttcagtgaccaaaatttttaaaggctatctggata-----ttttgcacagTTAAGTATGAAGCAAGGCTTGAGGATGGAACAGTTGTATCGAAATCTGATGGTGTTGAGTTCACTGTGAGAGATG
















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|11274712|gb|BF325047.1|BF325047
EST:     ACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGCATGAAGTGTTTTG                         TTA-GTTTGAAGC
genomic: ACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTT-Ggtacgaaact ... ttttctacagTTAAGTTTGAAGC
EST: gi|208257351|gb|GE056206.1|GE056206
EST:     TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTG                         TTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCAT
genomic: TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTGgtacgaaact ... ttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCAT
EST: gi|209705418|gb|BW668037.1|BW668037
EST:     TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTG                         TTAAGTTTGAAGCTAGGCTTGA
genomic: TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTGgtacgaaact ... ttttctacagTTAAGTTTGAAGCTAGGCTTGA
EST: gi|192314623|gb|FK006381.1|FK006381
EST:     TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTG                         TTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATG
genomic: TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTGgtacgaaact ... ttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATG
EST: gi|192314622|gb|FK006380.1|FK006380
EST:     TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTG                         TTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATG
genomic: TACTGAAGGGGAGAAATGGGACAATCCTAAGGACCTGGATGAAGTGTTTGgtacgaaact ... ttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagcaacactttcagtattgtttaaagtttccttctttctctcttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATGGGGTGGAGTTCACTGTGGAAGAGG
                      tttaaagtttccttct  CT-rich tract
                 tattgtttaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaaactctatcctttattgtctttgagaatcatctgtttagcaacactttcagtattgtttaaagtttccttctttctctcttttctacagTTAAGTTTGAAGCTAGGCTTGAAGACGGGACAGTCATTTCAAAATCTGATGGGGTGGAGTTCACTGTGGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG