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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT

Basic information

species Zea mays
transcript GRMZM2G025231_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 9
gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT
||||| ||||  ||||| |   || |  | ||       |  |   |  |||   ||| ||     || |   ||   ||| |||||   |    ||||||| |  ||||||||||| || |||||||||||||||||||||||||||||||||||  ||||||| ||||||||||||||||||||||| |||||||| |
gtaaatcttattcaactttcagttctgttccgt------atgcagttgctgtgatttgagc-----cttacatttcccttc-ctgttctgttg--tgcagCTTACGAATGTTGCCAGTCTCTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACTGGCATCCTGGAAATGAGATGGAGTGGTGTTGGCATTGATGATT

upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
---gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT
     | |   || ||||||      | || |||   |        ||  |||  ||  |   |  | ||   | ||| |    ||| ||||  ||  ||||||| |  |||||||| ||  |||||||  | || ||||||||||| |||||||| || |||||||| |||||||||||||||||||||||||||||||| |
gtatgagaatctaggcaactga----tttttttcagaatgcctccttaacttt--atgatacact-tatcctgaccttttccaaactttttc--ctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT

upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 13
gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgc--tgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT
     |  | |   |   | | || || ||  |           ||| |  | ||   |||| | | |||   | |  |    | |||  | ||   ||||||| |  || ||||| ||| |||||||  |||||||||| || || |||||||| ||  | ||||| ||||||||||||||||| |||||||||||||| |
-----gtatgaaacagcgttgcttcttattataatttttctgaaagtatcctttag-atgca-tatttga--ttaaaatcatttattttgtttgtaatgcagCTTAGCAACGTTGCTAGCTTGTGGTTTCTGTCACTTTTCATTTGTATTTTTGCAACTGGTATCCTGGAAATGAGATGGAGTGGAGTTGGAATTGATGAAT

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|32849550|gb|CD989231.1|CD989231
EST:     TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|94474954|gb|EB703912.1|EB703912
EST:     GGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32849428|gb|CD989109.1|CD989109
EST:     TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|67012262|gb|CO441011.1|CO441011
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32833246|gb|CD972924.1|CD972924
EST:     ACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: ACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32835222|gb|CD974900.1|CD974900
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32833958|gb|CD973636.1|CD973636
EST:     TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: TACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|67029021|gb|CO457770.1|CO457770
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|67014493|gb|CO443242.1|CO443242
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32856218|gb|CD995899.1|CD995899
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGGTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32928606|gb|CF033418.1|CF033418
EST:     GCACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|67018557|gb|CO447306.1|CO447306
EST:     CCTGCCATNNCTGTTTATGTGACAGGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: CCTGCCAT--CTGTTTAT-TGACA-GGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|94475064|gb|EB704022.1|EB704022
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|32916441|gb|CF021253.1|CF021253
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
EST: gi|71324690|gb|DR799051.1|DR799051
EST:     GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAG                         CTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT
genomic: GTACATTGCCTGCCATCTGTTTATTGACAGGGAAATTTATCACTCCAGAGgtaaagctta ... tctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT
                                        tttcatct  CT-rich tract
      tatattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA