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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcataacagaccatttgctgttatgaagaatttggaactgctgttcagattacatcttacaaaaactgataaaaccttgttctgcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 11
gtacttcataacagaccatttgctgttatgaagaatttg-gaactgctgttcagattacatcttacaaaaactgataa-aaccttgttctgcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG
             |   | |||||  || || | || || | |    | ||| | | ||  ||    || | || |   |||  |   ||||||||||||||| ||||| ||||||||||||||||| ||||| || || ||||| |||||||| ||||| | ||| |||||||||||||||
-------------gtatacttgctactacgatgcatctgtgtaactttcttcggttcacgactgg-gaatattgttgttaactatacactgcatctgcagGTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATG
















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|60342075|gb|DN209048.1|DN209048
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|211381837|gb|FL377365.1|FL377365
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|211506668|gb|FL391689.1|FL391689
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCA
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCA
EST: gi|50326819|gb|CO521945.1|CO521945
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|211487243|gb|FL369769.1|FL369769
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|50326828|gb|CO521954.1|CO521954
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|211542541|gb|FL409069.1|FL409069
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|67025362|gb|CO454111.1|CO454111
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60397137|gb|DN229953.1|DN229953
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60353904|gb|DN220877.1|DN220877
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|50326829|gb|CO521955.1|CO521955
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|88758266|gb|DY542407.1|DY542407
EST:     GATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: GATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|33942632|gb|CF349232.1|CF349232
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|4730397|gb|AI649563.1|AI649563
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|211466963|gb|FL423374.1|FL423374
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60355304|gb|DN222277.1|DN222277
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|40337526|gb|CK371596.1|CK371596
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|21621426|gb|BQ619432.1|BQ619432
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|40334154|gb|CK368224.1|CK368224
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|78022408|gb|DV490795.1|DV490795
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60339780|gb|DN206753.1|DN206753
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|88754474|gb|DY538615.1|DY538615
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTTTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|8102998|gb|AW927666.1|AW927666
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|37400365|gb|CF637533.1|CF637533
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTGTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60399063|gb|DN231878.1|DN231878
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
EST: gi|60355314|gb|DN222287.1|DN222287
EST:     ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTG                         GTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT
genomic: ACATGGGTCAAGAATGATAGGCCTCTGGAGGAAACCGACATTGTTCTCTGgtacttcata ... gcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttcagattacatcttacaaaaactgataaaaccttgttctgcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG
                         aactgat  putative branch site (score: 3)
                      aaaaactgataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcataacagaccatttgctgttatgaagaatttggaactgctgttcagattacatcttacaaaaactgataaaaccttgttctgcatctgcagGTACGTGTTCGGGCTCACCCATATCCCCAGGCTAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA