Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGAAATGGGTGGCGGGACATGGGATAGAGACACTGTACTACGTGCTCTGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatgattctttgtcctcgttactttctaggccttacatgcgatgaactttcagcgatttatgtgtgcccaggtacgtttaactagtgaacacatc...

Basic information

species Zea mays
transcript GRMZM2G061620_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061620_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
TCTTGAAATGGGTGGCGGGACATGGGATAGAGACACTGTACTACGTGCTCTGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatgattctttgtcctcgttactttctaggccttacatgcgatgaactttcagcgatttat--gtgtgcccaggtacgtttaac-tagtgaa-cacatc-
| | || |||||||| || |  |||||| | ||||||||| | |||||  | || ||||| | ||||||||| ||||| ||||| ||||||||||||||||||||  ||     || || |  |     | ||  |   |  ||   || |  || |  ||| |||  | ||  |     || |   |  || |||  || ||  
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaag--tgcacgcttatcattctgtaactgtaaacgaaatttg---tggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat
















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|76012358|gb|DT939528.1|DT939528
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|7216451|gb|AW562573.1|AW562573
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|33103619|gb|CF063579.1|CF063579
EST:     GTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: GTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|32944591|gb|CF049410.1|CF049410
EST:     ACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: ACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|4314922|gb|AI444722.2|AI444722
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GNGATTCCTGAACAAATGGAGGGTCCTGCACCGNCTCCGATTTCC-AACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|33103634|gb|CF063594.1|CF063594
EST:     GTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: GTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|101401583|gb|EB822467.1|EB822467
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|76280698|gb|DV020266.1|DV020266
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|211501745|gb|FL041143.1|FL041143
EST:     TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
EST: gi|76280697|gb|DV020265.1|DV020265
EST:     TCCAGAGCGTGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA
genomic: TCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGAGGTTCCTGCACCGCCTCCGAGTTCCCAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGAAATGGGTGGCGGGACATGGGATAGAGACACTGTACTACGTGCTCTGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatgattctttgtcctcgttactttctaggccttacatgcgatgaactttcagcgatttatgtgtgcccaggtacgtttaactagtgaacacatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT