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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag

Basic information

species Zea mays
transcript GRMZM2G137528_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaa----atat-gcacattctgatttgtgaacacaactttcag
||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||||||||||||| |  || |  |||| | |||      |    |||| ||||||||||| |  ||||| ||||||| ||
AGTTGATCCGTTGGTCAATCTTATGAAAGTTGAGAAGGTTCCTGATTCTACTTATGATATGATTGGAGGTCTTGATCAGCAAATCAAAGAGATCAAAGAGgtttgtatataatttcaatgtactattgatgcatcgcatatagcacattctgactcatgaactcaacttttag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag--------------------------------------------------------------------------------------------------------------
||||||||||||||||||||| |||||||||||||| ||||| |||||||||||||| |||||||| ||  | ||||||||||||||||| || ||||||||    ||||    | | |     |    ||  |  |  |   | | || | |  |  || |  ||                                                                                                                
AGTTGATCCATTGGTCAATCTGATGAAAGTTGAGAAAGTTCCCGATTCTACATATGACATGATTGGTGGTTTAGACCAGCAAATTAAAGAAATAAAAGAGgt--actttgcttgacattctttcaatgtcaggagttagatgcttttatctatccatgcatcactcgtgtgttacctttccgtgtgcatgtatctatctatttatattttagtgtagcatcatgcattagaaaaattagtttagtttttgaacctaatgtatgtgattaaatgtacag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgtt--ttga------------------actaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag-------------------------------------------------------------------------------------------------------------
||||||||||||||||||||| |||||||||||||||||||| |||||||| || || |||||||| ||  | ||||||||||||||||| || |||||||| ||||  ||||                  | | |||    ||     ||  |  |  | ||||| |  | |  |  || |  ||                                                                                                               
AGTTGATCCATTGGTCAATCTGATGAAAGTTGAGAAGGTTCCCGATTCTACTTACGACATGATTGGTGGTTTAGACCAGCAAATTAAAGAAATAAAAGAGgtatgttgcttgacattctttcggttttggcatttaaaattcgttctgtcaggagttagatattcttacctatccatgcatcactcgtgtgttaccttcctgtatgcatgtatctatcatgtatattttagtgtagcatcatgcattacaaaaatccgtttagtttttgggcctaatgtatgtgattaaatgtacag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattc--------tgatttgtgaacacaactttcag-----------
||| ||||| ||||| || || |||||||||||||||||||| || || |||||||| |||||||| || |||||||||||||| || || || || ||||| ||  | |    | ||   |     || ||||    |   ||         | | || |  | |  |  || |            
AGTAGATCCCTTGGTTAACCTTATGAAAGTTGAGAAGGTTCCAGACTCCACATATGACATGATTGGTGGTCTTGACCAGCAAATCAAGGAAATAAAGGAGgtatgcatagtgaaagaaacaaacgatactaaaagtcactggtttcatgcttttaaattttatataatatctttactggtttatcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg---------aactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag--------------------------------------
||| ||||| ||||| || || |||||||||||||||||||| || || || ||||| |||||||| || ||||||||||| ||||| || || || ||||| || || |         |||  |||   |   |||| | | |||   |  |||  | |||     || | ||                                         
AGTAGATCCCTTGGTTAACCTTATGAAAGTTGAGAAGGTTCCAGACTCCACCTATGACATGATTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgtttt----gaactaaa--------atgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag
||| |||||| |||| || || ||||||||||| || ||||| ||||||||||||||||||||||| || ||||| |||||||| |||||||| || |||||| | | |    || ||           ||    | |     ||||       |  |    |||    | | | |||||
AGTAGATCCACTGGTAAACCTTATGAAAGTTGAAAAAGTTCCGGATTCTACATATGATATGATTGGTGGTCTTGATCAGCAAATCAAAGAGATAAAGGAGgttagctatatgagagcttcttctgatttatttgttttggttgaaatccttctgtcttatgctgtct-taaacccttcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgt--tttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtg--aacacaactttcag------------------------------------------------------------------------------------------------------
||| |||||  | || || || ||||||||||| || ||||| || || |||||||| ||||| || || |||||||||||||||||||| || ||||||||||||  ||||| | |   |    | | |    | |||    |||   ||| |    |     || || |                                                                                                       
AGTAGATCCCCTCGTAAACCTTATGAAAGTTGAAAAAGTTCCAGACTCCACATATGACATGATCGGTGGTCTTGACCAGCAAATTAAAGAAATAAAAGAGgtttgtcctttgaccaattcttacatgttatttcattattattattaccattagcagcacttttaccttgatttaagttaggatttaaattcttaatctatagataagaaaggtatctcagatttttattttctcattttggtttaccttgtttttgttgtcttgatctttcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag------------------------------------------------------------------------------------------------------------
 || ||||| ||||| ||||| ||||||||||| ||||||||||| || || || |||||||||||||||||||| ||||||||||| |||||||||||||| ||   | |      ||    | | |    | | ||   |||    |||    ||  || | ||                                                                                                              
GGTGGATCCGTTGGTGAATCTTATGAAAGTTGAAAAGGTTCCTGACTCCACGTACGATATGATTGGAGGCCTTGATCAGCAAATTAAGGAGATCAAAGAGgtgtggacttaggatttattttattttattttattttgtttatttatttttcgttacttaaatctctctccttcctgttgtcagacctgttctgtgtgtttattccttttgatcaattattctgatgtatggccttgccataaaactcttctctgccgcgttgggtttttgggcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ20576 (Selaginella moellendorffii), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag
||| |||||  | || ||| | ||||| ||||||||||| || || || || || |||||||| || || |||||||||||||| |||||||||||||||||  ||||||  |||   |    | || |    |  |  |  |||| ||||    |      | ||||
AGTGGATCCTCTCGTGAATTTGATGAAGGTTGAGAAGGTCCCGGACTCCACGTACGATATGATCGGTGGGCTTGACCAGCAAATCAAAGAGATCAAAGAGgtcagttttgg-ctatgct----tttcccttcgaggttaagtttcttatttc---atttctttctcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ28638 (Selaginella moellendorffii), 5'ss of exon 3
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag
||| |||||  | || ||| | ||||| ||||||||||| || || || || || |||||||| || || |||||||||||||| |||||||||||||||||  ||||||       ||||  |  |     ||  ||    |||| ||||    |      | ||||
AGTGGATCCTCTCGTGAATTTGATGAAGGTTGAGAAGGTCCCGGACTCCACGTACGATATGATCGGTGGGCTTGACCAGCAAATCAAAGAGATCAAAGAGgtcagttttggct----atgcttttcccttcgaagttgagt-ttcttatttc---atttctttctcag

upper sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ04162 (Selaginella moellendorffii), 5'ss of exon 2
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag
||| |||||  | || ||| | ||||| ||||||||||| || || || || || |||||||| || || |||||||||||||| |||||||||||||||||  ||||||  |||   |    | || |    |  |  |  |||| ||||    |      | ||||
AGTGGATCCTCTCGTGAATTTGATGAAGGTTGAGAAGGTCCCGGACTCCACGTACGATATGATCGGTGGGCTTGACCAGCAAATCAAAGAGATCAAAGAGgtcagttttgg-ctatgct----tttcccttcgaggttgagtttcttatttc---atttctttctcag

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|32941875|gb|CF046694.1|CF046694
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|6989624|gb|AW447837.1|AW447837
EST:     TGGAGGTCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: TGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|19350715|gb|BM895247.1|BM895247
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|211070411|gb|FL012986.1|FL012986
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|67024358|gb|CO453107.1|CO453107
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|19350732|gb|BM895264.1|BM895264
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|60395128|gb|DN227997.1|DN227997
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|32866277|gb|CF005959.1|CF005959
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|32933070|gb|CF037882.1|CF037882
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA