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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA

Basic information

species Zea mays
transcript GRMZM2G074300_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g38000.1 (Oryza sativa), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
||||| | || ||| || || | | | | || | | ||||||| || | | ||||||||| ||||| |||||||||||||| ||||| || |||||||||||||||||||| || |||||||||||||||||||||||||||||||| || ||||
gtacg-gtgcagatccct--cgcagggtt-tcgattcgattcgattcgattctcctcgatctgatg-gtttttgttcatgtagTTCGTGAGCGATGGCGTGTTCTACGCGGAGCTGAACGAGATGCTGACGCGGGAGCTGGCCGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTGACGCCGA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcg-ctaccagccct-----tctcccccctgcgtcgatggat-------ctgacctgtgctcttgtcc----------gtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
||| || || | | || ||| || ||| | | |||| |||| || | | || | | || ||| | |||||||| ||||||||||||||||||||||| || ||| | ||||| || ||||| || ||||| ||||||||||| |||||||| ||||| || || |
gtaggccaggcttctgaatatgttgcggctgtgagcgcgggcggccggccccttgcgaggacaggtggctaagtctacgtattctattgctccatgtgccacacagTTCGTCCAGGACGGCGTGTTCTACGCCGAGCTGAACGAGCTCCTGACCCGCGAGCTGGCCGAGGATGGCTACTCCGGTGTGGAGGTCCGCGTGACCCCCA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------gtacgcga-gctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgt-agTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
| || | | | | | | || | || | | | | | || || | | ||||| | ||||||| ||||| || |||| |||||||||||| ||| | || || ||||| || || ||||| |||||||||||||| || |||||||| || || |
gtgaggctatctcgttttgtggaggttttccaggctcgtgttgatttgctctattctggcacggccttgcttctagaagctcacacagttgcattgtgggttggtctttgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGGGAACTTGCCGAGGATGGCTACTCCGGCGTTGAAGTGCGCGTGACCCCCA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------gtacgcgagctcctcctaaacgtagcgct-accagcccttctcccccctgcgtcgatgga------tctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
| | | | | | || || || | | | | || | | | || | | || | |||| || ||||| || |||| |||||||||||||||| | || || || |||||||| || || ||||| || || ||||| ||||||||||| || |
gtggaattcttcgcttgtgaacaagtttttgagactttggctgtttttttttttaaatgatttttaattgttttttttgctgaaaactcactagggcacatttcgagtagatcacagcactcatgtttgttttatctcttttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGCGAGCTCGCCGAAGATGGCTATTCTGGAGTGGAAGTGCGCGTCACTCCCA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtacgcgagctcctcc-taaacgtagcgctaccagcc--cttctcccccctgc--gtcgatggatctgacctgtgctcttgtccg--tagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
| || || || ||| | ||| | || ||| | | ||| | ||| ||| | | | || | | ||||||| || || || |||| || ||||| || ||| | || || ||||||||||| || || || ||||||||||| |||||||||||||| || |
gtgtgtgtaacccatcatcgctcttttctgcaaatctgataatactaccctgcttggttcacttgctcactgctggttctcccttccctttttctatgagcagTTCGTAGCGGATGGAGTTTTCTTTGCGGAGCTGAACGAGCTCCTCACCCGGGAGCTCGCCGAAGATGGGTACTCCGGCGTTGAGGTGCGCGTCACCCCCA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------gtacgcgagctcctcctaaacgta-gcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgc----tcttgtccgt--agTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
| | ||| | || || | | || || | | | |||| | |||| ||| | || |||| || ||||| ||||| | || |||||||||||| | || || || ||||| || ||||||||||| ||||| ||||||||||||||||| || |
gtttgtggttctaatttcaggcacttcgaaatttcgagatacttgaggttgtgagggttttttagtattacgttttgttgcccgatccttttgaaagttttacagctctgccgtgtgtctggtctcggtcgcgcagTTTGTAGCAGACGGTGTGTTTTTTGCTGAGCTCAATGAGCTTCTCACCCGAGAGCTTGCTGAGGACGGCTATTCCGGAGTGGAGGTGCGCGTCACGCCTA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
| | || | | | | ||| |||||||| ||| || |||||||||||||||||||||||| | || ||||||||||| |||||||| || ||||| |||||||||||||| ||||||||||
---------------------------------------gtttgtcaagcaatgccgctccctcctctgattctctcttccagTTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGGGAGCTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34304 (Selaginella moellendorffii), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
|| | || | ||||| ||| | | ||||| || |||| |||||||| ||| ||||||||||||||||||||||| ||| | || ||||||||| | || ||||| || ||||| |||||||||||||| ||||||||||
---------------------gtctgttcagcaatgccgctccctccttctcc------tctgatttg-attctt----ccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
|| | || | ||| ||||| | | ||||| || |||| |||||||| ||| ||||||||||||||||||||||| ||| | || ||||||||| | || ||||| || ||||| |||||||||||||| ||||||||||
---------------------gtttgttcagcaatgccgctctccccttc------tgctctgatttg-attctt----ccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31296 (Selaginella moellendorffii), 3'ss of exon 1
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
|| | || | ||| ||||| ||| ||| |||| ||| |||||||| ||| || |||||||||||||||||||||||| | || ||||||||| | |||||||| || ||||| |||||||||||||| ||||||||||
---------------------gtttgttcagcaatgccgctctcccct-----------tctcctctgatctctcttcc--agTTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGGGAGTTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

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|211516716|gb|FL197113.1|FL197113
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|149078913|gb|EE167734.2|EE167734
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211504917|gb|FL197047.1|FL197047
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTATTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211507278|gb|FL197062.1|FL197062
EST:     CCCATCTTCCTCCGTTAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211504910|gb|FL197040.1|FL197040
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|148955372|gb|EC900934.2|EC900934
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211098262|gb|FL316231.1|FL316231
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGC-GAGGCTCAATGAGATGCTGACGCG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAG-CTCAATGAGATGCTGACGCG
EST: gi|211012588|gb|FL327135.1|FL327135
EST:     CCCATCTTCCTCCGTTAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211514358|gb|FL197097.1|FL197097
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGC-GAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211507277|gb|FL197061.1|FL197061
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|94479335|gb|EB708293.1|EB708293
EST:     CCATCTTCCTCCGTCAACCATGGCGACCCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACCGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCG
genomic: CCATCTTCCTCCGTCAACCATGGCGACCC-AGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGAC-GGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCG
EST: gi|78111606|gb|DV530003.1|DV530003
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211502560|gb|FL197032.1|FL197032
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|18661874|gb|BM501626.1|BM501626
EST:     CCCATCTTCCTCCGTTAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCG-CAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211372195|gb|FL196976.1|FL196976
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCS-AGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211372197|gb|FL196978.1|FL196978
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|9254139|gb|BE344607.1|BE344607
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
EST: gi|211377526|gb|FL197016.1|FL197016
EST:     CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAG                         TTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG
genomic: CCCATCTTCCTCCGTCAACCATGGCGACCCAGATCAGCAAGAAGAAGAAGgtacgcgagc ... ttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA
                              atctgac  putative branch site (score: 3)
 ctcttgtcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG