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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcac-tgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                   ||||      ||  | |        |||    |    |   |    |  || |          |    |       ||| ||||    ||   |||         || ||||||||||| ||||| || ||||| ||  | ||| | |||||||| |||||||| || |||||| ||||||||||||| || |||||||| || || || |
-------------------------------------------------------------------gtttgtggcttaaaattgaatattcattcaggttgaccgtgtacatttcaaacacaattatttttcatatgctccctctattgaagcttgtgatttacacatgaattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAACTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagt-cactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaatt--ttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                |  |||    |  ||| | |  |   ||   ||  ||  |      | |     ||||| |   || |||   |     ||  |   | |  | || |||||||| || |||||  | ||||| ||  |  || ||||||||||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
-------------------------------------------------------------------------------cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaag-caaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                      |  || ||| ||| | | |    ||  |   |      ||  |   ||  || ||| |   ||||         |  || ||| |  ||   || ||   || |||          ||| |||||||| || || ||  | ||||| ||  |  || ||||||||||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
------------------------------------------------------ttatttaagccttatgt-ctgcataccaccct------atactcacaaaaca-tgtaca--aagcaaaagaaaacctttgaaagacatt---ttaatcaatgtatt----------cttgcagGTTATAGGAATCGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                ||||   |||  ||   |||  ||    |  | ||  ||      |   ||| |  || | |  | |   | |   ||||||||    ||             |  ||| ||     | |||  | ||||||||||| ||||| || ||||| ||  | ||| | |||||||| |||||| | || |||||| ||||||||||||| || |||||||| || || ||||
-----------------------------------------------gtttgtggcttaaaa---ttgaatatt--ccttcagattgaccatgtacatttcaaacattattattttt-catatgctccctctattgaag-----------cttatgatttacacatggat--tgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 8
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                          ||||  |  | |  ||  |  || |  ||  | ||    ||||   |  | |  |     |||||  ||     |||  ||  ||   ||  |  |||| ||||||||||| ||  | || ||||| ||| |  || ||||||||||||| || ||||| ||||||||||| ||||| || || ||||||||||| || || |
------------------------------------------------------------------------agagcttatgatcttatgccaccttctatagaga-tgcagagtaaaaatcacataacga--aaaaaacttttcaaagatatgttgatcaagtcat--tcttgcagGTTATTGGAATCAATTTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTTCGACTTGCAATAATAGAATATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
          ||| ||   || | | | |     |     | ||||  |  || |   |||   | |||||        |||  |  ||   | | |||||| |  |  | ||    |||   | ||| | ||||         || ||| |  |  ||||| |    || |  ||||||||||| |||||  |  |||| ||| |  || | ||||| |||||||||||||| || ||||| |||||||||||  | ||||| ||||| ||||| |
---------gtttgttacaacagaaatacccaaaccagatcatgccaat--ggcttcatgataacatgttt-----tgtttaaaagactttcactcttttaacttgcctttctc---gcc---catccatattcag-------ttgatgacttctatattttat----atgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaccattttttgtt-actggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgtttt----gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
          |||  | || ||    || ||   |  |||    | | ||  |  ||| |    ||     |            | |       |||  | |||||| || |   |   |      | | |  || |   | || |  | ||   |  ||||| |||      |  |  ||||||||||| |||||  |  |||| ||| |  | || |||||||||||||||||||| || || |||||||||||||| || || || ||||| ||||| |
---------gtttgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                  || || || |  | | ||  ||   |    |   |   |     |   |||        ||  |||| |   |||||| | ||||       ||||||||||| |||||  |  |||| ||| |  || |||| ||||||||||||||||| |||||| |||||||||||||||| ||||||||||| |||||  
----------------------------------------------------------------------------------gtttgttgcatctctcttgtgtgctttagatactacttttattgcttcctt-------atttagttggtgactgaattatctttta---cggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                         |  | | |  | ||    ||| | |  |||        | |   ||     ||| | |  || ||   ||||  |||| | |     | |  ||  | || | |||           ||||||||||| | |||  | || |||||| | ||  |||| |||||||| || |||||||||||||| || ||||| || || ||||||||||| ||||| |
---------------------------------------------------------tccatgacaagcttcagggctttaaagatgtccatgcatgtgagagg---agtcttatgtgcatg--ttcccctttcagaca----ttttaaataagcgattcttg-----------cagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                        |||  |  ||  |   || |  ||||  | | |    ||||| ||        |  |  |       |||  | |   ||  || || || || ||    ||||||| ||||| |||||  |  | || ||| |  | || || |||||||| || ||||| |||||||| |||||||| || |||||||||||||| || ||||
----------------------------------------------------------------------gcccaaattctacaaa--tgaatcttttccatggctgaatcctgaaaaatacaattttcattagtgttcagtatt-tcttttcatgcatatttttctg----ttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA

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|31356310|gb|CD440667.1|CD440667
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|211334572|gb|FL404959.1|FL404959
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGSTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|40336631|gb|CK370701.1|CK370701
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|116828872|gb|EC861659.1|EC861659
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAG-TTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|32914759|gb|CF019571.1|CF019571
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|24763712|gb|CA398883.1|CA398883
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACC
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACC
EST: gi|211206781|gb|FL154157.1|FL154157
EST:     TAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|32849162|gb|CD988843.1|CD988843
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|32919959|gb|CF024771.1|CF024771
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|37393714|gb|CF634122.1|CF634122
EST:     TTCCAGATGTTCGGGTTAACATAATCAGCAAGCTTGATCAGGTTTATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|32849378|gb|CD989059.1|CD989059
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
EST: gi|31361222|gb|CD445579.1|CD445579
EST:     TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAG                         GTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA
genomic: TTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                         ttttgat  putative branch site (score: 4)
                                               tctttc  CT-rich tract
                                  aattttgttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA