Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcactccgaacacagccatgtcagtgcgggtgaaaggaagctcgttttatagaacctttttttgttgttgttgttctgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACAGGGACACCGAGGAGC

Basic information

species Zea mays
transcript GRMZM2G152447_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152447_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 4
-----------------gtgcgcactccgaacacagccatgtcagtgcgggtgaaaggaagctcgttttatagaacctttttttgttgttgttgttctgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACAGGGACACCGAGGAGC
                  |   |||| | || |||  |   ||  |||   | |    ||    ||  |       || | | | |  ||||         |   ||||| | ||||  || |||||||||||||||||||  |||||||| |  || || ||||| |||||||||||||||||||  ||  | |||||| ||||||
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgca--tcagcaaaactctgtaatgagatgactgtctatatgattgt------atcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
















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|50328960|gb|CO524086.1|CO524086
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|211512568|gb|FL110029.1|FL110029
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|71436322|gb|DR817372.1|DR817372
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|18169298|gb|BM339138.1|BM339138
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|116817885|gb|EC860795.1|EC860795
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|24934165|gb|CA452383.1|CA452383
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|149107456|gb|EE189334.2|EE189334
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|91876187|gb|EB406144.1|EB406144
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|78109968|gb|DV528383.1|DV528383
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|78109969|gb|DV528384.1|DV528384
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|78086366|gb|DV514759.1|DV514759
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|76288593|gb|DV028161.1|DV028161
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|91872645|gb|EB402602.1|EB402602
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTA
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTA
EST: gi|211512569|gb|FL110030.1|FL110030
EST:     CTGGAGAGGGGTGGCGCCTCGAGGCAAGTACATT-GCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: CTGGAGAGGGGTGGCGCCTCGAGGCAATTAC-TTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|78110599|gb|DV529007.1|DV529007
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|71312265|gb|DR792656.1|DR792656
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|116828633|gb|EC859889.1|EC859889
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|101394597|gb|EB819233.1|EB819233
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
EST: gi|56461959|gb|CK986257.1|CK986257
EST:     ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAG                         GATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT
genomic: ACTGGAGAGGGGTGGCGCCTCGAGGCAATTACTTAGCCAATTTGCTGAAGgtgcgcactc ... tgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggaagctcgttttatagaacctttttttgttgttgttgttctgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACAGGGACACCGAGGAGC
                                       ttgttct  CT-rich tract
             ttttatagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcactccgaacacagccatgtcagtgcgggtgaaaggaagctcgttttatagaacctttttttgttgttgttgttctgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACAGGGACACCGAGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG