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

GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc...

Basic information

species Zea mays
transcript GRMZM2G075719_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcac-----gcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc
|||||||||||||||||| || ||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||     |  | |     |  || |||   | | |||   |    || |  ||| | |||   |     ||  ||||   | |  |  ||| |   ||    
GCTCGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGACAAGTTCGACAACACCTACCAGgtgcgttcttcttctctatcggtttcgccg--tctgctcgcctctcttcggggggttggggttggatctgatcg--ggggccagatccggcggtggcgccctgg-

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtg-ttatcttcccgcgtcggggttgggtttgtgggttggatccaatc-
 || || ||||||||||| || ||| |||| || ||||| || || || || ||||||||||| ||||||||||| || || || ||||||||||| |||||  ||       |||   |||| |   |   |  |        ||| |     || | |            |  |     |   ||   ||    | ||  
TCTTGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCTGTGGGAAAAACTAGCATCATCACTCGCTTCATGTATGACAAATTTGACAACACTTATCAGgtctgatcagatccac-tatctcagccactttttaagtttcaatgtgtttcctttgatcagggaaataaaatgacgacaaatgc-tgcactgctaaccatta

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtg-ctgttcgtgttatcttcccgcgtcggggttg--ggtttgtgggttggatccaatc
 ||||| ||||||||||| || ||| |||| || |||||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| |||||               ||  ||  |     |    | | | || |  |  ||  | || ||    |      | | |   |||||    || ||||      
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg---

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcct----ctccgatcccgatcgatccctcgcgtgctgttcgt--gttatcttcccgcgtcggggttgggtttgtgggttggatccaatc
  | ||||||||||||||||||||| |||| ||||| ||||| ||||| |||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||     ||  |  |||    ||| |||||    | |  || |         || |  |||| ||      | |         || ||        | ||   
TTTAGCCAAGTACAAGCTCGTCTTCTTGGGTGACCAATCCGTGGGCAAAACCAGCATCATCACTCGCTTCATGTACGATAAATTCGATAACACCTATCAGgtacgtttctccctaaccctaaccctcagatccaatcctaaaccgcatcgagaactcctaagttagctctttatggctaaaaccacttcgtaaacc---ttca---

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcga---tccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc-
  | |||||||||||||||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| || |||||  | |      |    | ||| |||||    | |   | | |||    || |    |||| ||      | |     |   ||  |        | || || 
TTTAGCCAAGTACAAGCTCGTCTTCCTGGGTGACCAATCCGTGGGCAAAACCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccctaaccctaaccctcagatccaatccaaaactgcatcgaaaactata-aagttagctcttaaaggctaaaatcacttcttaaacc---ttcactct

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcg-tcggggttgggtttgtgggttggatccaatc--
 ||||| ||||||||||| || ||| |||| || || ||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| ||||| |  |  |   ||   |    |  ||     | ||  |   |    | ||      |  |||  | | ||  ||||      ||||  |||   || |   
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGCGATCAATCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgt-cttcttctttcagatccaatctctctttcactatttcat-cacattttttaaaaaaaattcaagagatcacggttttacc-gtggaatgggatcattgct

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgt-tatcttcccgcgtcggggttgggtttgtgggttggatccaatc-
 ||||| ||||| ||||| || || ||||| || || ||||||||||| ||||| ||||| || || ||||||||||| || |||||||||||||||||||||  |   ||      |   ||        |||    |   ||  |  ||| |  | ||| ||   |  |    || |||    |     || |   ||  
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgta-aatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcc-cagggtttgattg

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgg-gtttgtgggttggatcc-aatc--
 |||||||||||||||||||||||| |||| ||||| |||||||| ||||| ||||||||||| || ||||||||||| || ||||||||||| || |||||   |    |   | |  ||| |  |    ||||||     ||    |  | |  || | ||   |  |  |  |||| |    |  ||| |||||  |||  
TCTCGCCAAGTACAAGCTCGTCTTCTTGGGAGACCAATCCGTCGGAAAGACTAGCATCATCACTCGATTCATGTACGACAAATTCGACAACACCTATCAGgtcaaa---tctttatggatctgct-tgtttatcgattttcagcaattttgttggtttgtgttttggttttagttttggtgcgaatttgtttgatcccgatcct

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc-
 || ||||| |||||||| |||||| | ||||| ||||| ||||| || |||||||||||||| || ||||||||||| || ||||| || || || ||||||   |    |       |      | | ||||        || |  | || |  ||   ||   |      | |||  |  |   | || ||  |    
TCTGGCCAAATACAAGCTTGTCTTCTTAGGGGATCAGTCTGTCGGGAAAACCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaattctttgcgattatgtcttcggatccgcgatctgcttctttttaggtttgggtttgtgttatttgattgc-tgagaaagctgtatagagaaa

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 2
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc
                   ||||||||||| |||||||| || |||||||||  |||||||||||| |||||||| || |||||||| ||||| |||||||| ||     | || |   ||    |   ||| | |  |||  | |||| ||   ||   | | | |                                 
-------------------GTCTTCCTGGGAGACCAGTCTGTGGGCAAGACCTCCATCATCACCCGATTCATGTATGACAAGTTCGATAACACGTACCAGgtgcg-tactctgcgcatttcctttacaacga-caacgcctgacatgcttttgcggtctccgtgcag---------------------------------

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc
||| || ||||||||||||||||| || || || ||||| || || ||||| ||||||||||| || |||||||| |||||||| |||||||| ||||||||| ||  |    |  |  ||| |  || |  |    |      |   | |||  |                                            
GCTTGCAAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatga--gattacgagtttcttctctctcactttggcaaattggaaattttcaag--------------------------------------------

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 1
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc
||| || ||||||||||||||||| || || || ||||| || || ||||| ||||||||||| || |||||||| |||||||| |||||||| ||||||||| ||  |    |  |  ||| |  || |  |    |      |   | |||  |                                            
GCTTGCGAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatga--gattacgagtttcttc--tctcactttggcaaattggaatttttcaag--------------------------------------------

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|211109341|gb|FL282964.1|FL282964
EST:     TCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAG                         GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: TCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggc ... tggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     CCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAG                         GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggc ... tggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     CCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAG                         GCTACAGTTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggc ... tggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgttatcttcccgcgtcggggttgggtttgtgggttggatccaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc