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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaacctctatctcagaatcaaatgcatagggaaatggatcttctgtcctttaaccggaaaaagtttatccgtagttcgagcattagtcgtggttgtaattatgcgtattttgcatgtgggaaggagcttatgtcggatttaccacggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCCAAGCGGTATCTTGAGGATGTGTGTGCCCACAAGCAAGCTATTCCCTTCC

Basic information

species Physcomitrella patens
transcript PP1S38_376V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S38_376V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 3'ss of exon 3
gtaccaacctctatctcagaatcaaatgcatagggaaatggatcttctgtcctttaaccggaaaaagtttatccgtagttcgagcattagtcgtggttgtaattatgcgtattttgcatgtgggaaggagcttatgtcggatttaccacggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCCAAGCGGTATCTTGAGGATGTGTGTGCCCACAAGCAAGCTATTCCCTTCC
                                                           || |    |   | |   |||   ||  |||   |  |  ||  |    | ||||   ||           || ||||    |||  ||      ||||||||||  | ||| ||||    || || | | |  ||    |||  ||||||||| |||| ||||||||||||  |||||||||||||||||| |||||||
-------------------------------------------------------ggttggtagttatcccttctatgttaatgctatagcatt--tcttagctgc-tgcatttgttattcttttgttgtctaatgttcttttt-tcatacaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCCAAGAGGTACCTTGAGGATGTGATTGCCCACAAGCAAGCTATCCCCTTCC
















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|37823698|gb|BJ581764.1|BJ581764
EST:     CAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37832499|gb|BJ590511.1|BJ590511
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162203216|gb|FC379313.1|FC379313
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37849607|gb|BJ607615.1|BJ607615
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162248381|gb|FC420906.1|FC420906
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18370115|gb|BJ201717.1|BJ201717
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37841187|gb|BJ599195.1|BJ599195
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGC-AGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162202837|gb|FC379819.1|FC379819
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162237079|gb|FC413238.1|FC413238
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18368504|gb|BJ200589.1|BJ200589
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37850940|gb|BJ608948.1|BJ608948
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162251657|gb|FC426063.1|FC426063
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162276406|gb|FC452656.1|FC452656
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162271900|gb|FC448110.1|FC448110
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162237080|gb|FC413239.1|FC413239
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162213580|gb|FC389452.1|FC389452
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37848210|gb|BJ606218.1|BJ606218
EST:     CNTGCAAGGCCAGAGGGTCGAAATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCG-GATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18344500|gb|BJ176540.1|BJ176540
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162202838|gb|FC379820.1|FC379820
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162248380|gb|FC420905.1|FC420905
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162217445|gb|FC393121.1|FC393121
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162177227|gb|FC352656.1|FC352656
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18364022|gb|BJ196095.1|BJ196095
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGC-AGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18360355|gb|BJ192417.1|BJ192417
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162272416|gb|FC449055.1|FC449055
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162196966|gb|FC373332.1|FC373332
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162203215|gb|FC379312.1|FC379312
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18371592|gb|BJ203194.1|BJ203194
EST:     CCTGCAAGGCCAGAGGGTCGAATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37851774|gb|BJ609782.1|BJ609782
EST:     CCTGCAAGGCCAGAGGGTCGAATTTGCGAGTGCACTTCAAG                         AACACTAGGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTA-GGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGC
EST: gi|162217446|gb|FC393122.1|FC393122
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162269116|gb|FC444984.1|FC444984
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162271899|gb|FC448109.1|FC448109
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|18355556|gb|BJ187615.1|BJ187615
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|37838498|gb|BJ596506.1|BJ596506
EST:     GGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: GGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162251656|gb|FC426062.1|FC426062
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCCCTTCAAG                         AACCCTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
EST: gi|162262697|gb|FC438479.1|FC438479
EST:     CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAG                         AACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC
genomic: CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCACTTCAAGgtaccaacct ... ggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgtattttgcatgtgggaaggagcttatgtcggatttaccacggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCCAAGCGGTATCTTGAGGATGTGTGTGCCCACAAGCAAGCTATTCCCTTCC
     tatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaacctctatctcagaatcaaatgcatagggaaatggatcttctgtcctttaaccggaaaaagtttatccgtagttcgagcattagtcgtggttgtaattatgcgtattttgcatgtgggaaggagcttatgtcggatttaccacggtggtgcagAACACTAGGGAGGCAGCGCAAGCCATAAAGCATATGGAGTTGGCGAAGGCCAAGCGGTATCTTGAGGATGTGTGTGCCCACAAGCAAGCTATTCCCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT