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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaacttcaccaattggtcttgacgtaacacactatcttggttgcag

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 4
CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaacttcaccaattggtcttgacgtaacacactatcttggttgcag
|| || || |||||  ||||||| |||||||| ||| |||| | ||||||||||||||| || ||||| || |||||||||||||| |||||||||||||| | || || |    |   |||    ||| | |||                  ||||  |     |  | | ||||| ||||| |||||||   || |||
CTGTTAGAAATGCTCATGAATAACTGCGGAGAACCTATCCACAAGCAGGTCATTGATAACGGTCTTCTCCCGATACTTGTGAAGATTGTGAAGAAAAAGgtgatttgttctcttttctttttccc-tggaagttgga----------------ggaaggttgttga--gatgttgacttaacatactatctgtatttcag

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 5'ss of exon 3
CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatttttcactgaatttatta-tggcaattgtgaaacctgttctcatttggaacttcaccaattggtcttgacgtaacacactatcttggttgcag
 ||||||||||| |  ||||||||   ||||| ||||| || || ||||| ||||||||||| || || || ||||| ||||||||||| |||||||||||   || ||   ||   |  | |||  |||| |||     | ||||| | | ||| | ||  |     |  ||||  | |  ||||               
TTATTGGAGATGTTGATGAATAATATTGGAGAACCTGTTCACAGACAGGTGATTGATAATGGGCTCCTCCCTATACTAGTGAAGATAGTAAAGAAAAAGgtgtttttttccccaagaacatgatttctggccatt-----aactgtttttagttgaagctaaatttgcttatcttttc-tctcacag--------------
















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|71421501|gb|DR805467.1|DR805467
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|50325447|gb|CO520573.1|CO520573
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|78107223|gb|DV525641.1|DV525641
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|93017403|gb|EB642923.1|EB642923
EST:     CATTGATAATGGCCTTCTTCCCATACTTTGTGA-GATAGTGAAGAAAAAG                         ACGGATTTTAC-AGTTCGAGAAAAAATATTTCTTCTGTAAGATGCAACACA
genomic: CATTGATAATGGCCTTCTTCCAATACTT-GTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTT-ACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACA
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|93015305|gb|EB640825.1|EB640825
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTATATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|9953455|gb|BE640038.1|BE640038
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|71326005|gb|DR799685.1|DR799685
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|44682243|gb|CK787291.1|CK787291
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|148952813|gb|EC898805.2|EC898805
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|211276223|gb|FL230638.1|FL230638
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG                         ACGGATTTACCAGTTCGAGAAAAAATATCTCTTCTGTTAGATGCAACACAA
genomic: TCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatt ... ttggttgcagACGGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAGgtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaacttcaccaattggtcttgacgtaacacactatcttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA