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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
              |    | | ||   |||| || |||  | | |     | ||||    || ||  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||| |||||||
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttg-ctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
              |    | | ||   |||| || |||  | | |     | ||||    |||||  ||||| | |||    | |  ||  |||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||| | ||||||||||||||||| |||||||
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttg-ctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 25
------------gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctg-----tttcaattccgtcccaaaaatctgattcttgttgctc------tttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
              || | | |  |  ||   |||    | || |    ||||   |||   | ||     ||| ||| |  | |   ||   |  |  ||||||||       |||   |||||||| ||  |     | || || || || |||||||||||||| || |||||||| ||||| || ||||| || ||||||||  ||||||  || || |
gtctgcaattttcataccctattgtcaaatgcctacggtttcaatcttatttggtgagataacttgctggctttaaatgctattcagtaataatattgtttgttgcttggattttttattcagGCTGGCCACCTCAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCTGCTGTCAATGAGGCTTTGAATGAAATTTATGCTGAGGAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
  ||| |||  |||     |  |    |  | |    | | | | |  ||  ||    || ||       ||| |    ||     ||||      | ||||||||||  | | |||||||||||||||||||||||||||||| || ||||| |||||||| || |||||||| ||||||||| | ||||| || ||||
-gtaggatc--attagtggtaaaaattt--aattagatattagttgttgca-tgccataactctaatgggaaacttcactttaatatgct------atagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
  ||||||          | | ||| |  |  |    |||   |   | ||   |||| ||| |   | |  ||| |  | | |||      ||  | ||||||||||  | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | |||||  | ||||| || ||||
-gtagcattaatactgtcaacaatttcatct-taatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
            | | |    ||||     |     | ||  |||  ||   |||| || | || |  ||  |||  ||  | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||||||||| || |||||||| ||||||||| | |||||||| ||||
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 23
--------gttagcatctgattgaaaatctattc--ctgcagtgcactttgaatagaagcc----ctgtttcaa----ttccgtcccaaaa----atctgattcttgttgctctttggac---agGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
        ||     |||  ||   ||| | ||    |  | |   ||||   |  |        |||||| ||    ||   | | | |     || || | |||| |  | | |||     ||||||| ||  | |   | || || || ||  ||||||||||||| || || ||||| ||||| || |||||||| ||||||||  ||||||| || ||||
gtctgtaggtctcattctattttctaatgtgttaagttttaatcttcttttggtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttagGCTGGCCACATCCGATTGGTTAAGCCGTACTTGGTTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
  ||||||          | | ||| |     |    |||   |   | ||   |||| ||| |  |  |  ||| |  | | |||      ||  | ||||||||||  | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| |||||||  | ||||| || ||||
-gtagcattaatactgtcaacaatttc-attttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 25
--------gttagcatctgattg---aaaatctattcctgcagtgcactttgaatagaagccctg-----tttcaattccgtcccaaaaatctgattcttgttgctc----tttgga----cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
         ||   | |  ||||   ||   |||    | || |    |||| | |||     ||     ||  ||| |  | |   ||   |  |  ||||||||     |||  |    |||||||| ||  |     | || || || || |||||||||||||| || |||||||| || || || |||||||| ||||||||  ||||||| || || |
gtctgcaatttcataccctattgccaaatggctacagtttcaatcttatttggagagataatttgctggtttcaaatgctattctgtaatagtattgtttgttgcttggattttttattttcagGCTGGCCACCTTAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCCGCTGTCAATGAAGCTTTGAATGAAATTTATGTTGAGGAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtc-ccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
||||| | |||| |||  |  |  |  |         |||  ||| || |      | |  | | |  |  || |  || ||  |  || |||     ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||| ||||| || ||||| ||  |||||||| | || || ||||| |
gttagaagctgactgatgactttgtttt---------tttctataaaaac---aactgagctacattacttaacaattggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
gttagcatctgattgaaaatcta----ttcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
|||||   ||||      || ||    || |||      ||||   |     | | |      | ||  |  |  |    |  |||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||||||||| || ||||||||  |||||||| | ||||  ||||| |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaac---aatctatatctgatgattatttcttgtttctgatc--tcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 25
-------------------------gtta-gcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttg-ctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
                         || | | || |   ||      | ||   |  |       ||| || |||           ||  |||      |||| || ||| |   ||||||||    |||||||||||  | ||||||||||| || ||||||||||| ||||||||||  |||||  |||| || |||||||| || ||||   || |||| || ||||
gtctgcatgtttgcttactctttatgtgatggatattgctgtgtgcttcttttagtgggaacaaatgattaaaagtttaaaaatggttttgtcaatggtatcttatgcttatgatctctttgggtttcagGCTGGTCACCTTCATCTTGTGAAGCCCTATATGGTTGCTGTTCAGAGTACTAATGTGGCTGCGGTAAATGAAGCATTAAATGGTATTCATGTAGAGGAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
----------------gttagcatctgattgaaaatctattcctgcagtgcact--ttgaatagaagccctgtttcaattccgtcccaaaaatctgattct-tgttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
                | |    | |         |||  | ||| |||    |  |||  |    | |   | |  |         |    | || || |  |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||| | ||||||| || ||||
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG

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|67012270|gb|CO441019.1|CO441019
EST:     TGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAA                         GCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC
genomic: TGCTTGCACTTCGTTTAGATCACACCATAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|67024143|gb|CO452892.1|CO452892
EST:     TGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC
genomic: TGCTTGCACTTCGTTTAGATCACACCATAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|67014840|gb|CO443589.1|CO443589
EST:     TGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC
genomic: TGCTTGCACTTCGTTTAGATCACACCATAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
                            atctgat  putative branch site (score: 4)
                                  ttcttgttgctcttt  CT-rich tract
         tttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG