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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 1
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
|||| | |    || | |  | ||| ||||||| |||   |  | |  || |                  |   |||| ||             |||||| |  |||| ||| |||||||||||||||| || |||||||||||||| ||||||||||||||||| |||||||| || |||||||||
gtaagcatc---ctccccgccttccttccttccttccttccttccgccacca------------------ccatcctcaccct-----------cctcctccgcctcccgcc-cgcagTTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 1
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaag-gctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
                                     |||  |    |   ||  ||    |  | ||   ||  |   ||    |      ||| || ||||  || ||| | ||||||||||| | ||  ||||||||||||| ||||| ||||| |||||| | |||||||||||||||| ||||
-----------------------------------gtaattactaatatataacaataataataataattactttctctgctattcgctcgttgatcttcttct-cttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
gtaatcctgtcgcttctcctcctccctccttccctccaatcgc-cggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgac-ctgacctcc--ttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
||| ||        ||||   ||| |||  || |||  ||| |          || | | | || ||||     || || | ||   |    || |  | |  || | ||||     ||||||||||  ||||  | ||||| ||||| ||||| |||||||||||| | |||||||| || |||||||||
gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 1
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
                                            | ||    ||     | || |          ||| |  |   |  |||      ||||  || ||    ||||||||||| ||||  |||||||| |||| ||||| ||||| |||||| | |||||||||||||||| ||||
--------------------------------------------gtaattctatttataataataatcacactctctctctgctatttgcctattgatcttcttcttctctgtcgcagTTCAACATCCCCAACCTCCGCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 1
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
                   |     |||  || ||| |  |  |    ||   |  | || ||| ||| |    || ||||||           |    || | ||||     ||||||||||| ||||  | ||||||||||| ||||| |||||||||||| | |||||||| ||   |||||||
------------------gtaagtactctctctctctacacatc----actttttttttataac-caacgaccaccgcgcctcttacttttcctctcattttccctccaaattcgcagTTCAACATCCCCAATCTCCGCGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATACCGTCAAG

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|211359331|gb|FL325567.1|FL325567
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|71327563|gb|DR800390.1|DR800390
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211542143|gb|FL390828.1|FL390828
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211218538|gb|FL338330.1|FL338330
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211114226|gb|FL350275.1|FL350275
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211217973|gb|FL307283.1|FL307283
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|71303539|gb|DR787880.1|DR787880
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|8367294|gb|BE050239.1|BE050239
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211362192|gb|FL333555.1|FL333555
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCSTYGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211316704|gb|FL359227.1|FL359227
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211105804|gb|FL320712.1|FL320712
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211283545|gb|FL347777.1|FL347777
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211064773|gb|FL350726.1|FL350726
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211078718|gb|FL360383.1|FL360383
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211414492|gb|FL334083.1|FL334083
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211381249|gb|FL356117.1|FL356117
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
EST: gi|211467481|gb|FL327941.1|FL327941
EST:     GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGG                         TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC
genomic: GCCTGCAGGATGGCATCTCCCGCCACTCCTTCGACACCCCGCTGTACCGGgtaatcctgt ... tgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
                         acctgac  putative branch site (score: 3)
                               cctccttccgctcctg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC