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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaaaatacctttcttgctgttgctgcacactagtattctcagaggtttcttgtacagttgtacttaatttagttgttcacgttagtctatgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT

Basic information

species Zea mays
transcript GRMZM2G007721_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007721_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g04254.1 (Oryza sativa), 3'ss of exon 12
----tctaaaatacctt-tcttgctgttgctgcacactagtattctcagaggtttcttgtacagttgtacttaatttagttgttcacgttagtctatgatt-gcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT
    |  |||| |     ||| || | || ||  |     || | |  | | |   |  |  |  || | | | ||    |   |  |    | | ||||| | |||| || || ||||||||||| ||||||||||||||||| |||||||| ||||| |||||||| |||||| |||||||||  ||||| ||||||||||| |
cagttgcaaaaaatagggtctggcaggtggtgtgc-----tactttttgggctaattcttgaaaatg-attcagttctcctaacctagcctttgtgtgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGACCGAGTGCATGCTAGAGGGGTAGGGCCTCTACCTATACCAGTTGATCAAT
















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|5915157|gb|AW052798.1|AW052798
EST:     GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCG                         TGTCCTACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
genomic: GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCGgtaagtgctc ... atgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
EST: gi|60345023|gb|DN211996.1|DN211996
EST:     GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCG                         TGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
genomic: GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCGgtaagtgctc ... atgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
EST: gi|71433445|gb|DR814495.1|DR814495
EST:     GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCG                         TGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
genomic: GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCGgtaagtgctc ... atgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
EST: gi|60399301|gb|DN232115.1|DN232115
EST:     GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCG                         TGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
genomic: GTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCGgtaagtgctc ... atgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
EST: gi|113701297|gb|EE678801.1|EE678801
EST:     GGTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCG                         TGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC
genomic: GGTGCATCATGGTGGTGCTGGAACGACAGCCGCAGGTCTTAAAGCAGCGgtaagtgctc ... atgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcttgtacagttgtacttaatttagttgttcacgttagtctatgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT
                  acttaat  putative branch site (score: 4)
              ttgtacttaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaaaatacctttcttgctgttgctgcacactagtattctcagaggtttcttgtacagttgtacttaatttagttgttcacgttagtctatgattgcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - ttcttgc
- - - - - - - - - - gttgctg