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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctcttgtaaaaattccttttttggtcattgagctccagcaataacgaagttcctaatagtctgatttgttattctttgatttgatcatatgcttgacag

Basic information

species Zea mays
transcript GRMZM2G086489_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 13
CAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggct-cttgtaaaaatt-----ccttttttggt---------cattgagct-ccagcaataacgaag-------ttcct--aatagtctgatttgttattctttgatttgatcatatgcttgacag
   ||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||||  | | |||||| |||||      || | |   |          ||||   | || ||||| || | |       |||||  |  ||| ||| || ||  || |  |    |  || | |||   ||
---GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtag
















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|22491259|gb|BU051182.1|BU051182
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|40334433|gb|CK368503.1|CK368503
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32943853|gb|CF048672.1|CF048672
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCTTCTGGAATATAGCGAAGAATGCAGTTGGGCTCACATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32929744|gb|CF034556.1|CF034556
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|67026638|gb|CO455387.1|CO455387
EST:     TGTTC-ACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: TGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32929783|gb|CF034595.1|CF034595
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32929509|gb|CF034321.1|CF034321
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32835080|gb|CD974758.1|CD974758
EST:     CTTCACCACCAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|19437266|gb|BM953676.1|BM953676
EST:     CTTCCCCAACAGGAAGGATCCNCCAAGGAGTTTGTTCAACATGGATGAAG                         AATCCAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctt ... tgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctcttgtaaaaattccttttttggtcattgagctccagcaataacgaagttcctaatagtctgatttgttattctttgatttgatcatatgcttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA