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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT

Basic information

species Zea mays
transcript GRMZM5G826714_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtc-tagattttatagcagaga--gggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
   |||  ||    |||    |  | ||  ||          ||| |  | || | || ||    |      | ||||||||| | | |   | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||                              
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
ctaatcgcag--atagtcctaggaagaattccatacaagttgcacttttgt-ctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
 ||| |   |  || |   || ||  | ||  ||     ||  | | || | | |||  || |  |      | ||||||||| ||| |  || ||  |||||||||||||||||||||||||||||| || |||||||||||||||||||||||| |||| |||||||||||                              
-taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatt-tctctttattgattcttaaca-agataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctag----attttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
     |  |     ||  |  ||  | |   |   ||||   ||||    ||||    ||     | |  ||   |  |||||||  |   |  ||||| ||||||||||||||||||||| ||||||||||| ||||||||||||||||  || ||    |||||||| || ||                              
----ccatacgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttat-tgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctag----attttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
     |  |     ||  |  ||  | |   |   ||||   ||||    ||||    ||     | |  ||   |  |||||||  |   |  ||||| ||||||||||||||||||||| ||||||||||| ||||||||||||||||  || ||    |||||||| || ||                              
----ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttat-tgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT--------------------------------------------------------------------------
                                            || || |  |    | ||    |      |||||     | ||  |||    |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | ||| |||| |||||                                                                          
-----------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatatttt--tggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
 ||  || | |  |||| ||  |  | |   |   ||||   | ||    ||||            |    |||     ||  |   |  |||||  ||||||||||||||||| || ||||||||||| ||||||||||||||||  || ||    ||||| || || ||                              
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
---ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
     |||   | | | |   ||     | |   ||  |||   ||| |     |  | |   |    |     | | |||||      || ||||| ||||||||||||||||||||| |||||||| || |||||||| ||||| || ||||| || || ||||| || ||                              
gcttaaatttaaaacaattgaagtttacagttggtattagta--actatcagaaaattctggcaatttactatatccataacatcactcttgtttat-tgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
---cta-atcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
    ||      | | | |  |  ||  ||||  ||     |   |    ||| |   ||||  ||    |      |||||     | ||  |||    |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| |||||                              
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttt--tggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
ctaatcgcagatagtcctaggaagaattcca--tacaagttgca-cttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
 |  |   |  ||   | |   | |||| ||  |   |  || | || |   |||  | |   |          | |||||||    || |  || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||| || |||||||| || ||                              
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacat---cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatct------gcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
   |     |  || |  |   | |||     | || |||   | ||     |  |||| ||            |||||  |   | ||||  | |      |||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||  | || ||||| ||  |                              
---aggatggcaagacacattgacaat---ggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatctaatcttcctgtcctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC

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|4610038|gb|AI600877.1|AI600877
EST:     GCCTACGAAGTTTTTCACCGCGGACGGGCGCAGGGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACGAAGTTTTTCACCGCGGACGGGCGCAGGGCAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT
                           tcttaac  putative branch site (score: 2)
                                         ttctttatct  putative PPT
     tagattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT

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