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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCGCCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACACGGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcacatttaccctgttggcgtaggaatctgcagagcatacagtttgcgaactgacaccagtcgtctttacaaacttggcaaatgcgaagctgacctgaactcatagaagctgcatccatgatccatcttaccag

Basic information

species Zea mays
transcript GRMZM2G159285_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159285_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
GGCGCGCCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACACGGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcacatttaccctgttggcgtaggaatctgcagagcatacagtttgcgaactgacaccagtcgtctttacaaacttggcaaatgcgaagctga--cctgaactcatagaagctgcatccatgatccatcttaccag
|| || ||||||||||||||||||||||||||||||||||||||||||| ||| |||||| |||||||| ||||||||||| ||||||||||| || | |||||||| |          | | |   |||| |||||||    |||| ||   ||||   |            |  || |||   ||||| ||| |    || ||| | ||  || |    | ||||| ||    |  |||
GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgc----------tggccacgggaacctgcagaa---acagattatcaactagta------------attaatttg---aatgcaaagtttgatccggaattgatgaaaacactgtgcatgaacctctctgtcag
















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|37384582|gb|CF629379.1|CF629379
EST:     GGAACTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|71757626|gb|DR955563.1|DR955563
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|37381992|gb|CF627908.1|CF627908
EST:     GGAACTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|20208504|gb|BQ134593.1|BQ134593
EST:     GAGCTCTCCGTTGCTCTGAAGAAGATGTTCAAGCACCTTCACCACATCCG                         GGANCAACATGAATGACNGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GAGCTCTCCGTTGCTCTGAAGAAGATGTTC-AGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|37381948|gb|CF627882.1|CF627882
EST:     GGAACTCTCCGTTGTTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|8576974|gb|BE129611.1|BE129611
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACTTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|12047139|gb|BF729278.1|BF729278
EST:     TTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: TTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|71771347|gb|DR969284.1|DR969284
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|71760459|gb|DR958396.1|DR958396
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|6056635|gb|AW091040.1|AW091040
EST:     GGAGCTCTNCGTTGCTCTGAAGAAGATGNTCAGCACTTTCACCACATCCG                         GNAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|91054479|gb|EB164897.1|EB164897
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|78544346|gb|DV621844.1|DV621844
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|14203793|gb|BG837470.1|BG837470
EST:     GGAACTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|18181502|gb|BM382712.1|BM382712
EST:     TCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: TCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|76020197|gb|DT947367.1|DT947367
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|78108965|gb|DV527382.1|DV527382
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|78119357|gb|DV537741.1|DV537741
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCCCCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|76285970|gb|DV025538.1|DV025538
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|78180321|gb|DV550694.1|DV550694
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACTTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTGGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
EST: gi|18181098|gb|BM382308.1|BM382308
EST:     GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCG                         GGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG
genomic: GGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcaca ... atcttaccagGGAACAACATGAATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCGCCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACACGGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcacatttaccctgttggcgtaggaatctgcagagcatacagtttgcgaactgacaccagtcgtctttacaaacttggcaaatgcgaagctgacctgaactcatagaagctgcatccatgatccatcttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG