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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgctgaccttgttcatatcggtttctttgttttgtagtcagttttgctgtgcagagttactcttctggtttgcctaattttaaaggaaaaaaaactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG

Basic information

species Zea mays
transcript GRMZM2G017853_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017853_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g26920.2 (Oryza sativa), 3'ss of exon 7
gtaactgctgaccttgttcatat--cggtttctttgttttgta-gtcagttttgctgtg---cagagttactcttctggtttgcctaatt--ttaaaggaaaaaaaa----------ctttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG
|| | ||||   ||  ||  | |  |   || |||||||  || |||   || ||||||   ||    | | ||  | | |   |   |   | ||  |||| ||||          |||| ||||||||||||||||||  |||||||||  |||||||||||||||||||||||   ||| |||||||
gtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcagGCAAGAAATAATGGACTCTGTTAACAGAAGTGGAAAATTTGACACGAAGTTCCAAGGTTTTACTG
















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|74233405|gb|DT641319.1|DT641319
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATG
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATG
EST: gi|211291636|gb|FL460652.1|FL460652
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|18177348|gb|BM378558.1|BM378558
EST:     GGACTGCGGAGTCGAATATTTATGGGCTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|76927174|gb|DV171165.1|DV171165
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|71310881|gb|DR791743.1|DR791743
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|78089273|gb|DV517647.1|DV517647
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|71308383|gb|DR790420.1|DR790420
EST:     CGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: CGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|74233404|gb|DT641318.1|DT641318
EST:     GGACTGCGGAGTCGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|211289510|gb|FL460651.1|FL460651
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAACCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|76927172|gb|DV171164.1|DV171164
EST:     GGACTGCGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|91051135|gb|EB161553.1|EB161553
EST:     GGACTGGGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|71764490|gb|DR962427.1|DR962427
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCT
EST: gi|78085441|gb|DV513834.1|DV513834
EST:     GGAATGGGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagagttactcttctggtttgcctaattttaaaggaaaaaaaactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG
                        gcctaat  putative branch site (score: 3)
                           taattttaaaggaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgctgaccttgttcatatcggtttctttgttttgtagtcagttttgctgtgcagagttactcttctggtttgcctaattttaaaggaaaaaaaactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG