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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctctatcttctccatgttttgtcgatcggggatgtccatgttcttggccccatcaccattccatgggtggagcgcgctgatgatcctcggtctgcggcccggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACGACAAGGTGTTCGACTGGTCGCTCAAGGCCAAGATGATGGGCAAGAAGGC

Basic information

species Zea mays
transcript GRMZM2G102231_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102231_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g14580.1 (Oryza sativa), 3'ss of exon 1
gtatctctatcttctcc-atgttttg---tcgatcggggat------gtccatgttcttggccccatcaccattcca---tgggtggagcgcgctgatgatcctcggtctg------cggcccgg------------ggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACGACAAGGTGTTCGACTGGTCGCTCAAGGCCAAGATGATGGGCAAGAAGGC
|| ||||  ||| |||| | | || |   ||    | | ||      ||   | |  |||    | |      ||||   ||| |||||   | |||||||    ||  ||       |||  ||            || |||||||||||||| ||||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
gtctctccctctcctccgacgattcggtttcatatgcgcattcgatggtttctttctttgctttcttggttgctccaatttggatggagttgggtgatgatggatggattggatgaatggcgtggttgttgctggtgggtgcagACACGGAGGGGTTCTACACGGAGGTGCAGGAGAAGATCCTGGCGAGGTACGGCAAGGTGTTCGACTGGTCGCTCAAGGCCAAGATGATGGGCAAGAAGGC
















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|50338090|gb|CO533216.1|CO533216
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|148994252|gb|EE034006.2|EE034006
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|149013687|gb|EE043137.2|EE043137
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211019679|gb|FL048024.1|FL048024
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|148954135|gb|EC899536.2|EC899536
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAAAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211016901|gb|FL048018.1|FL048018
EST:     GAGGGCCAGTATYTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211016903|gb|FL048020.1|FL048020
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|71773066|gb|DR970984.1|DR970984
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCGCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211016905|gb|FL048022.1|FL048022
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211019680|gb|FL048025.1|FL048025
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|89250658|gb|DY622444.1|DY622444
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGGCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211019681|gb|FL048026.1|FL048026
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|13237285|gb|BG355299.1|BG355299
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|211016902|gb|FL048019.1|FL048019
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
EST: gi|60346823|gb|DN213796.1|DN213796
EST:     GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCG                         ACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG
genomic: GAGGGCCAGTATCTCGCACGTCATCTTCGATATGGACGGCCTTCTCCTCGgtatctctat ... cggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattccatgggtggagcgcgctgatgatcctcggtctgcggcccggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACGACAAGGTGTTCGACTGGTCGCTCAAGGCCAAGATGATGGGCAAGAAGGC
                    cgctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctctatcttctccatgttttgtcgatcggggatgtccatgttcttggccccatcaccattccatgggtggagcgcgctgatgatcctcggtctgcggcccggggcgcagACACGGAGGGCTTCTACACGGAGGTGCAGGAGAAGATCCTAGCGAGGTACGACAAGGTGTTCGACTGGTCGCTCAAGGCCAAGATGATGGGCAAGAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG