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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata...

Basic information

species Zea mays
transcript GRMZM5G826714_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 5'ss of exon 2
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcc--tagcaggccctggtct-attctattgag-tagtccagtcgacctgtac-aata-ta-
| |||||||||||||||||||||||||| |||||||| |||||||||||  | ||||| |||||||||||||| || || |||||||| |   ||| |        |   ||| ||||||||| | |   ||    ||  |  | | ||| ||| ||  | |||  |     |   || |||| || 
AAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTTgtaagtagcacatccatca-------ttcgtatctttcatctcaacctattattgagcgataattttattttatagaaattgtcttgcaatgcaaaactaatagtat

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g32110.4 (Oryza sativa), 5'ss of exon 2
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata-
||||||||||| |||||||||||||||| |||||||| |||||||||||  | |||  ||||||||||||||| ||||| |||||||| |  ||||| |||| |  || || | | |  | | |   | |  |   ||   |  ||  | ||       | | |        | ||| |  
AGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTTgtaagtagcaaccccacaccaaaaaatgcatct-tgtattgttcgttcaaaaaaatccatctgcatcttgtttccccaactattattaggccataatttta

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g32110.2 (Oryza sativa), 5'ss of exon 1
--------------------AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata-
                    ||||||||||| |||||||||||||||| |||||||| |||||||||||  | |||  ||||||||||||||| ||||| |||||||| |  ||||| |||| |  || || | | |  | | |   | |  |   ||   |  ||  | ||       | | |        | ||| |  
TTTTTGTTTTCCTCTTGCAGAGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTTgtaagtagcaaccccacaccaaaaaatgcatct-tgtattgttcgttcaaaaaaatccatctgcatcttgtttccccaactattattaggccataatttta

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G04210.1 (Glycine max), 5'ss of exon 2
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatattt-catctccagcctagcaggccctggtctattctattgagtagtc-cagtcgacctgtacaatata---
| ||||||||| | || |||||| |||| || ||||| || ||||||||||||||    ||||| |||||||| ||||| |||||||     |   |    |||| |  |  ||||   ||||  |||  | ||     |   | |||  |     | |||  |   |   |   |  | |    
AAGCTTATGATCCACTTGATCCATATGGAAATATCACAATCAAATGGGATATCATAAGTTGGACCCCTGATGGTTATGTTgtaagta-----ctttcttttacagtttcacctattaatatctgaagcaaatcatctgatttacaattaaacatgatggtcgtaaatgtttttggctcttttttc

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G50760.1 (Glycine max), 5'ss of exon 2
-AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata--
 | ||||||||| |||| || |||||||| || ||||| || ||||||||||| ||    ||||| |||||||||||||| ||||||| | |        ||| | |    | || ||       |  | | |   |  | ||  ||| |     ||  |    |   ||| | |  |     
GATGCTTATGATCCGCTTGACCCAAATGGGAATATCACAATCAAATGGGATATTATAAGCTGGACCCCTGATGGATATGTggtaagtatagtttttttgacaatatcaccttttaatttga---aaagcaaaccatctgttgtgcattatgcatggtgttgttttgctccttttctttccgtt

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata
| || |||||| |||| |||||| | |||||||| || || ||||||||| | |||   |||||||||||||| ||||| ||||||  ||     |||  |  ||  | | |||||    ||   |  || | |    || |  ||   |     | ||    |||| ||          
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaaga---acctga--agtagaaaatattaggcctt--gtttaccggtttttgattcatctaaactgtttgtttgttcgatctag--------

upper sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 2
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgag-tagtccagtcga--cctgtacaatata---------
| || |||||| | |||||||| ||||| || ||||| || ||||||||||| |||   |||||||| ||||| ||||| |||||||   ||  ||            |||||| ||| |  | |   || ||||    |    |    || | | |  |  |||  |  | |||  |   ||         
AAGCCTATGATGCACTGGATCCCAATGGAAATATCACGATCAAATGGGATATTATGAGCTGGACTCCAGATGGCTATGTTgtaagtact-tgttcat-----------tatatacttcctaactaatataacaggggtcgactcagataatagtgatcttgtagttcatgcttgtgtatgttaagtttaggt

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|50337724|gb|CO532850.1|CO532850
EST:     ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTC                         GCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACCT
genomic: ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaa ... cctcctgcagGCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACCT
EST: gi|88748730|gb|DY532871.1|DY532871
EST:     ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTC                         GCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACCT
genomic: ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaa ... cctcctgcagGCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACCT
EST: gi|76017849|gb|DT945019.1|DT945019
EST:     ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTC                         GCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACC
genomic: ACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaa ... cctcctgcagGCTGTTGTCACAATGTTTAATTATCAACAATTTCGGCATATCGGCGCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccaccc