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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT

Basic information

species Zea mays
transcript GRMZM2G107082_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
gtaccgcagatttgggaattttttatttgcca---gctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataaga-aatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
|||    ||||      |   || | ||| ||   | |||| ||  ||||   |      |     ||    |  ||   |  |||||    |  | |||||||||| | | |||||||||||||||||||||| |||||||| || || ||||| || ||||| ||||| |||||||||||||||||||||||| |||||||||||||||||||
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 4
gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgata-agaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
|||    ||||      |   || | ||  ||  ||| || |  |   | |||   ||||   || |  |  ||   |  |||||    | |  ||||||||||   | ||||||| |||||||||||||| |||||||| || || ||||| || ||||| ||||| |||||||||||||||||||||||| |||||||||||||||||||
gtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaa-taaacgtattggtctatcatgtatccataacaatatgctcccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
                                               | | |||     |  | | |   ||||  ||  | | || | |||    ||  | | | | |||||||||| |||||  |  | ||||||||||| |||||  |||| ||||| || || ||||||||||||||| | |||||  | |||||||||||    ||
---------------------------------------------gtgcactgcc----ttacgaaacagcctgcatt--cttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ37257 (Selaginella moellendorffii), 3'ss of exon 5
gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
                                               | | |||     |    | |   ||||  ||  | | || | |||    ||  | | | | |||||||||| |||||  |  | ||||||||||| |||||  |||| ||||| || || ||||||||||||||| | |||||  | |||||||||||    ||
---------------------------------------------gtgcactgcc----ttatgaaacagcctgcatt--cttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT

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|211124407|gb|FL002541.1|FL002541
EST:     ACSCGGAAAAAWTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTTYTTGARATGAATCCGTTCACCATGGTCAATGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTC-TTGAGATGAATCCGTTCACCATGGTCAATGGG
EST: gi|32928214|gb|CF033026.1|CF033026
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|89759015|gb|DY687974.1|DY687974
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|14243577|gb|BG841276.2|BG841276
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|32846052|gb|CD985733.1|CD985733
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|211124415|gb|FL002549.1|FL002549
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGG
EST: gi|33093807|gb|CF053801.1|CF053801
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|32941416|gb|CF046235.1|CF046235
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|148996106|gb|EE035369.2|EE035369
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|71769087|gb|DR967024.1|DR967024
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|211123625|gb|FL002524.1|FL002524
EST:     ACGCGGAAACATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCT
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCT
EST: gi|32942668|gb|CF047487.1|CF047487
EST:     GAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: GAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|211123624|gb|FL002523.1|FL002523
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|33100741|gb|CF060701.1|CF060701
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|89758437|gb|DY687616.1|DY687616
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|6012698|gb|AW062135.1|AW062135
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|148953532|gb|EE153041.2|EE153041
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|33094495|gb|CF054489.1|CF054489
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|32928697|gb|CF033509.1|CF033509
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|32858269|gb|CD997950.1|CD997950
EST:     GCGG--AAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCNCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGG
genomic: GCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTT--CCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGG
EST: gi|148941766|gb|EC886727.2|EC886727
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
EST: gi|33104066|gb|CF064026.1|CF064026
EST:     ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG
genomic: ACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcaga ... ccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
                          tgttgat  putative branch site (score: 4)
                                           ctccatctcc  putative PPT
                            ttgataagaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT