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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgaatgaccaagtcatggatttcctagaaccagggataccgtgcatctgctccttgctatcaatgtgaaactcaagtatctgcattgttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os03g64219.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64219.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 8
ttgtgaatgaccaag-tcatggatttcctagaaccagggataccgtgcatctgctccttgctatcaatgtgaaactcaagtatctgcattgttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAG
 | |    |||   | |||| |  | |      ||     ||  ||   | ||    |   |||  || ||||||||||||   |||| |   |||||||||| ||||||||||| |||||||||||||||||||||||||| || || ||||| || |||||||||||| |||||||   |||||
atttctgggactgggatcatagtatactattggccctttttattgtatttttgtgtatatatat-gatatgaaactcaagtgcgtgcacttgcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG
















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|29671297|gb|CB667572.1|CB667572
EST:     GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|88840178|gb|CI079632.1|CI079632
EST:     GAACGGGTAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|33681506|gb|CF309745.1|CF309745
EST:     GAACGGGGAGTGGGGTGACCACGTTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACG-TTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|87019141|gb|CI297342.1|CI297342
EST:     GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|88842564|gb|CI081820.1|CI081820
EST:     GGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|86418296|gb|CI032505.1|CI032505
EST:     GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
EST: gi|88840177|gb|CI079631.1|CI079631
EST:     GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT
genomic: GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatga ... ttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatctgctccttgctatcaatgtgaaactcaagtatctgcattgttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAG
                                          ttgtttttt  CT-rich tract
                                         attgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgaatgaccaagtcatggatttcctagaaccagggataccgtgcatctgctccttgctatcaatgtgaaactcaagtatctgcattgttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAG

- gtgaatg
- - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - -ccgtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atctgca