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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG

Basic information

species Zea mays
transcript GRMZM2G391936_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------------actatttgaagacag----gcatat---caccatcttagttatgtattcat--cctgcctcataatcttgtcccaaaat---cttga----cttga----tattatga--tgga---catttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                                                                             ||||  |  | |     ||||||        | ||| |||| |  | |    |  | |||  ||| ||||  ||| |   |||||    ||         || | |  | ||   |||| ||||| |||||||||||||||||||||||||| || |||||||| || || |||||||| || || ||| ||||||||||||||
gtaaggatttaacataataagttccatttggtagtgttctctaatattgcactattggcatcagatttacacaaatttattcaataataatactgcatatgtatgatgtattatttattttcttacaatcaacttcagtatcatgtcagaaactagccttgaacatctcaggcacagttgtaacctagaactcattgcagGCATATCTTTTCAATGATTACTGGGAAGACATAGGAACTATAAAATCATTCTTTGAAGCCAATCTTTCTCTTGCTGAACAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 9
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                      |  |    |   | | ||| |    |  || |  | ||| |  |  || |     || | | |  ||    ||  ||||||||||| |||||||||||||||||||| || || ||||| |  |||||||| |||||||| ||||| ||  |||| || 
--------------------gtatgactggaaaaaagcattaaggaggaatctt--ttttg-cttatgatttacctatggtgtgacaatttgtatg-cagGCTTATCTCTTCAATGATTACTGGGAAGACATAGGGACTATCAGATCCTTCTTCGAGGCAAATCTTGCCCTCACTGAGCAT

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgactt--gatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                             |   |    |       | |     |||||| |  || |   || ||    | | | |  ||    ||  ||||||||||| |||||||||||||||||||| || || ||||| |  || |||||||||||||| ||||| ||  |||| || 
--------------------------gtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtatg-cagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 9
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctca-taatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
          | |||  | ||   ||| |||   |   ||| |       | | |||  || |  |||    |  ||  ||| || |||         ||||||||||| || ||||| |||||||||||||| ||||| || |  || ||||| ||||| || ||||| ||  |||| || 
----------gtcagtaacatt--catattaagcacacatttaagtccaatgactaacgttatatcaagggat-aacaagattttttgag--------cagGCTTATCTCTTTAATGACTACTGGGAAGATATAGGAACAATAAGATCTTTCTTCGAGGCGAATCTTGCACTCACTGAGCAT

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 9
----------actatttgaagacaggcatatca--ccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacattt-cagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
          ||||| | ||       ||   |  ||||     ||||  |   ||  ||     ||   | | | |    | || |  | | |  |      || ||| ||||||||||| || |||||||| |||||||| ||||| || || |  || |||||||| ||||||||||| ||| ||| ||| 
gtctggatcaactatctaaaatattttattcaaacccatgaacattataaacaaatgatgatgggtacattcgacacttc-tgttcatctaacaacacacgacacttttgcagGCTTATCTGTTTAATGATTATTGGGAAGACATTGGTACAATCAGATCATTCTTTGAAGCAAACCTTGCCCTTACTGCACAT

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 3'ss of exon 8
---actatttga---agacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
   ||  |  ||   | | | |  | |     |  | |  | ||    || ||   ||| ||   ||      |||      || ||| | |         | ||||| ||  | || ||||| || ||||||||||||||||| ||||||||||||||||| || ||  | |||||  |||  |||
ccaaccttcagatttatagaagattctagatcttcttgagacgttactattctagttcaaaagtgtgagatgcaataactcattaatactgt------ttgtgcagGCGTACTTGTTTAATGACTATTGGGAAGATATTGGAACCATTAAGTCCTTCTTTGATGCCAATTTAGCTCTCACTGCTCAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 3'ss of exon 7
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaa----tcttgacttgatattatgatggacattt-cagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
          | |   | ||||   |  || || | | ||      |   |  |   |   |  || ||    |||    || | ||| || |     ||  ||||| ||| | |||||||| |||||||| ||||||||||| || ||||| |||||||| || ||  | |||||| ||   |||
----gcccctgtccatcttatccaaaatttggtga-gcatcagctattagttcttggcagattgcagaaattatctgccattaaaattttgttttgttttcgcagGCATATTTGTTCAATGACTACTGGGAGGATATTGGAACCATCAAGTCTTTCTTTGATGCTAATTTAGCTCTTACTTCTCAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                                    ||    |   ||  |       |||||    | |||   | | | | |      || ||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || || |||||  |||  |||
------------------------------------gtgggaagtttgtgt----gctttgtcttgcattctacgcctaaaactt-----gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 9
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                            |  |   |   |      || ||   | |||   || ||||      |||||||||             ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || || |||||  | |  |||
---------------------------gtgggaagttcgtgtgctttgtcttgcattctacccctaaaa------cttgatattg------------cagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACCGCTCAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ04435 (Selaginella moellendorffii), 3'ss of exon 8
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatatta-tgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                                       ||  || | | |     |||||    |   |       |  ||| |     | |  |  ||||||||| | || |||||||||||||| || || || || |||||||| |||| ||| ||||| ||||||||| ||   |||
--------------------------------------gttggtctttcgtttgtctcttggtgaatggttgctctgtactatcaacagcgtagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATTAAGTCGTTCTATGAAGCAAATCTTGCTCTTACTTGCCAG

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|32934983|gb|CF039795.1|CF039795
EST:     ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAG                         GCTCATCTTTTCAATGATTACTGAGAAGATATTGGAACTATTAAGTCCTTC
genomic: ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|13126505|gb|BG317075.1|BG317075
EST:     ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAG                         GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
genomic: ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     AAAGAAATCGATGTAAAG                         GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
genomic: AAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAG                         GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
genomic: ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|32934981|gb|CF039793.1|CF039793
EST:     ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGGAAAG                         GCTCATCTTTTCAATGATTACTGAGAAGATATTGGAACTATTAAGTCCTTC
genomic: ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAG                         GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
genomic: ATTTTGGTTCTGAAATAATTCCTGCTTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     TTCAGCAAAAGAAATCGATGTAAAG                         GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC
genomic: TTCAGCAAAAGAAATCGATGTAAAGgtacgtccgt ... gacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
                               ttgatattat  TA-rich tract