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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgcacggtcgaatttcttggttagatcctgagttctctctgtccttgttctccccttccccttggattggactgtgttgacacccttcttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATTAAATCTCCTGCAAATCAGGTGGAGTACCTGAAGCATTTCAGGGCAGATA

Basic information

species Zea mays
transcript GRMZM2G075488_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075488_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g06820.1 (Oryza sativa), 3'ss of exon 1
gtaagaatgcacggtcgaatttcttggttagatcctgagttctctctgtccttgttctccccttccccttggattggactgtgttgacaccc-ttcttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATTAAATCTCCTGCAAATCAGGTGGAGTACCTGAAGCATTTCAGGGCAGATA
        | |   || ||| | || | |||||  || ||| | ||  || |||||| |  ||| |||||       | || | |||||    ||  | ||| ||||| ||||||||| | || |||||||||||  ||||||||||||| ||||| | |||| | ||| | |||||||||||  |||||||||||||||||||||
--------gtagaatccaatatgtttggtagatgatgtgttttatccttctttgttcacatcttgccctt-------attgcgctgacattgatttgtatttgcagCGAGGAACAGGACTGTCAACACCGTTGACAACATCATCTCTTTCCCAAATAACATCTGCAGCAGAACAGGTGGAGTATTTGAAGCATTTCAGGGCAGATA
















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|71430371|gb|DR811421.1|DR811421
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
EST: gi|148934529|gb|EC878571.2|EC878571
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
EST: gi|31910752|gb|CD651581.1|CD651581
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
EST: gi|149107818|gb|EE292179.2|EE292179
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
EST: gi|149075976|gb|EE164545.2|EE164545
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
EST: gi|148995979|gb|EE035228.2|EE035228
EST:     GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAG                         CGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT
genomic: GGTGGTTAAAGAAAGCTTGTGAAGACCACCGCGTTGTCCTGCTAGATCAGgtaagaatgc ... ttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttctccccttccccttggattggactgtgttgacacccttcttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATTAAATCTCCTGCAAATCAGGTGGAGTACCTGAAGCATTTCAGGGCAGATA
                               tgttgac  putative branch site (score: 3)
                                     cacccttcttgttttc  CT-rich tract
                                             ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatgcacggtcgaatttcttggttagatcctgagttctctctgtccttgttctccccttccccttggattggactgtgttgacacccttcttgttttcagCGGGGAACAGGATTATCCACACCGTTGACTCCATCATCTCTTTCGCAAATTAAATCTCCTGCAAATCAGGTGGAGTACCTGAAGCATTTCAGGGCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT