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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG

Basic information

species Glycine max
transcript GLYMA14G04890.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 23
gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtc------agACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
       |  | |  ||   | || |  | |      ||  | |  |           | ||  ||||| || || |      ||||||| || || ||||| || || || || ||||| || ||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || ||||
------gtatattcttctttatttgcgacataagcactacatgaccattgggcttatattttattttcacgcctggcttttgcagACTTCTGACATCTTGTATTACGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACTCTTAAAGTTGCATTCCACCATGCAACTAAAGATG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 19
-----------------gtaattattgacttgtcccaactttcatcttgtttct---tatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
                  |   | ||   |||   ||  |  |||  | |||||   ||  ||||| |||||     |||| |  |       || ||||| || || |||||||| ||||| ||  | || || || ||||||||||| || ||  ||||||| |||||||||||||| |||||||| || |||||||
gttaacctttcacctctttttgtttttttttgggtcagttagcatagtttttctgcataggtaaaatacaaagggatttatactatctg---gtg-cagACATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
--------------------gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
                      | | | ||  || |  ||  ||  | | ||   ||||||||    ||     || ||  | |||   |      |||||||| ||||| ||||| ||||| || || ||||| || ||||||||||| ||  | |||||||| || ||||||||||| ||||||||||| || ||||
gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttcttt-----ccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 13
---------------gtaattattgacttgtcccaac-tttcatcttgtttcttat-ttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
                | |||||| | |     ||    | ||| |      |||   | |   |    || |  ||||    |  | |||  |||||||| ||||| ||||| ||||| || || ||||| || |||||||| || ||  | |||||||| || ||||||||||| ||||||||||| || || |
gtccaattctttttcttgattattcattaagtgcattactgcatttaaaacattacactgatttatgctactttctattttgatgcttcattccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGATTTGCAGCGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGACG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 23
gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcct--ttcatgcatgt------cagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
||||||  | || || ||||   || || |    |||  ||| | |   ||| | | || |   |  |  ||  || |      |||| ||||||| ||||||||||||||||| | ||||||||||| |||||||||||||| || |||||| |||||||||| ||||| |||||    ||||| |
gtaatttattacatggccca-tattaatgtatgctctgttttgacatggaaatccttttttcattgatcaatttatttttgggacagATTTCGGATGTATTGTACTATGAAGTATTGGACATCCCTCTTCCAGAATTACAAGGTTTAAAAACTTTGAAAGTTGCTTTTCATCATGCTGAAAAGGAGG

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|207763123|gb|GD735146.1|GD735146
EST:     AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAG                         ACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
genomic: AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAGgtaattattg ... tgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
EST: gi|16347912|gb|BI973507.1|BI973507
EST:     AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAG                         ACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
genomic: AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAGgtaattattg ... tgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
EST: gi|8283289|gb|BE020850.1|BE020850
EST:     AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAACCAG                         ACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
genomic: AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAGgtaattattg ... tgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
EST: gi|208283871|gb|GE088143.1|GE088143
EST:     AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAG                         ACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA
genomic: AGTATCGTGGTGTGGACCATTTGTCTGATATGCTGGTTCACTACAATCAGgtaattattg ... tgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG
                               tcttattcctttcat  CT-rich tract
        tttcttatttaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG