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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcctcttcatcttataatgtactataactttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

Basic information

species Glycine max
transcript GLYMA04G41600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
--------------------------------gtttggcctcttcatcttataatgtactataactttaacgtgaaagggatagatg-ctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
                                   |         ||||  || | || ||||  ||     | | || | |   || |   |  |||  || ||||||| ||||| ||||| ||||| ||||| |||||||| || || || |||||||| |||||||||||||| |||||||| |||||  |||| ||||| || |
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatt-tattatacttt--gtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 4
--------------------------gtttg---gcctcttcatcttata-atgtacta-taactttaacgtgaaagg---gatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
                          || ||    |  | | |  ||||| ||  || | ||| |||   |    |       || |  ||     ||||  | ||||||| ||||| |||||||| || || || |||||||| || || ||  |||| || |||||||||||||| |||||||| ||| |  |||| ||||| || |
gtcattcttcacctgctaggctagctgtgtgcatactacattactttatacataaacaactaattttgttgaactattttttgtataacctgtctatttctgtatgcagTCCTCAACCTATGGGAATGTTCTGGTGCTTGATGGTATTGTGCAGCTGACCGAAAAGGATGAATGTGCATACCAGGAAATGGTTACTCACCTTCCACTGT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
----gtttggcctcttcatcttataa-tgtactataactttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
     |||    |  | || | | || | ||   |  ||||  |       |  || |  ||  |  |||   | ||||||| ||||| ||||||||||| ||||| |||||||| || |||||||||||||| |||||||||||||| |||||||| |||||  |||| || || ||||
gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
----gtttggcctcttcatcttata---atgtactataact----ttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
       |   || |||||   | |   | | |  | ||||    ||  | |     |  |  |   |  |  | |   | ||||||| || || ||||| ||||| ||||| |||||||| || ||||| |||||||| |||||||||||||| |||||||| |||||  |||| || || || |
gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 4
-------gtttggcctcttcatcttataatgt--actataactttaacgtgaaagggatagatgctaat--cctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
        |||  |  |   ||||     ||   ||   ||||      | |  |   ||  |   | |  | ||||  || |||||| ||||| ||||| || || ||||| |||||||| |||||||| |||||||| ||||||||||| || |||||||| ||| |  |||| ||||| || |
gttatttttttatctgcgaaatctgcacgtgaaaacccgaactcgtcaatcattgtactaagtagcactttcatttctgttcgcagTCTTCAACCTATGGAAATGTTCTTGTGCTTGATGGTATAGTTCAGTTGACTGACAAGGATGAATGCGCATACCAGGAAATGGTTACTCACCTTCCACTGT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------gtttggcctcttcatct---tataatgtacta--taactttaacgtgaaagggatag---atgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
                                                ||||    | || ||||   | | |||| ||   |  ||||    |  |   | |||   ||||  || |||| |||| |||||| ||| | ||||| ||||||||||| |||||||| || ||||| ||||  ||||| ||||||||||| || ||||||||||| ||||| |||||||| |
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttattt-gcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

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|16997075|gb|BM086447.1|BM086447
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
EST: gi|22525271|gb|BU084082.1|BU084082
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
EST: gi|254325922|gb|GR838803.1|GR838803
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
EST: gi|254327481|gb|GR837104.1|GR837104
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
EST: gi|192295186|gb|FG986905.1|FG986905
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
EST: gi|298177837|gb|HO027390.1|HO027390
EST:     AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAG                         TCATCAGCTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT
genomic: AGATCTTATACAAGGAAAAGTCGGAGTACCAGGAGGTCTTGGTTTTTGAGgtttggcctc ... cattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtactataactttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT
                                 tgctaat  putative branch site (score: 2)
                                       tcctttcattttgc  CT-rich tract
       tataactttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggcctcttcatcttataatgtactataactttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA