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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG

Basic information

species Glycine max
transcript GLYMA04G12890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 5
-tgttgattgatgcatgtaagtgactccacctagtgggg--taaggtgtgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
 ||  | ||  |      |   |  |    ||    |    | || |||         ||  |   ||      |  | ||| |    | | | ||   |||||||||||||| || || |||||||||||||||||||| |||||  |||||||  |    ||  | ||||| |||||| || | ||||| ||||
gtgagggttcttcttatcatcagtttatgtcttacagatattgagttgtactacccaatatattgtttttggaaaaatgatactgacagatatatttgagcagTGGCTGCTCATCTGACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAATATCTTGTTTCCATGCAGAAAG

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 5
---------------------------------------tgttgattgatgcatgtaa-----gtgactccacctagtggggtaaggtgtgggtttttttagttgtattgcatgtatctaa---tattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
                                       | | | |   ||  |||       ||| ||   | |  |     ||        || |   || | | || | || ||  ||   || |  | | |   ||  ||||||||||||||| ||||| |||||||||||||||||||| |||||  |||||||  |    ||  | ||||| |||||| |||| ||||||||||
gtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttc-tggatagaaatgtactaaacgatgcttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
---------------------------------------tgttgat-tgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtatt-----gcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
                                       ||  | | |  | | |||   |       |  |      | ||   |    | | | || | ||||      ||    | || || || ||| ||||    ||||||||||||||| ||||| |||||||||||||||||||| |||||  |||||||  |    ||  | ||||| |||||  |||| ||||||||||
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcata--ctgtctgaggtatatttctggacagaattgtactaatcgatgatttc---gtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggttttttt--agttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
       | |    | | | | ||| ||  |  |    |||  |||   || ||||  |  || || | || |       |||||  | |||     ||||||||||||||| |||||||||||||| ||||||||||| |||||| |||||||||| |  |||||| | ||  || || | || ||||| ||||
------gtaagctttatta-tcacttcatatt-tatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgatttt---gtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
              ||    | |   |||  |      | |    |    ||  | |||  || ||  | |  || ||  | | |   |     |||||||||||||||| |||||||| ||||| ||||||||||| |||||| |||||||||| |  |||||  | ||  |||||  ||||||||| ||||
-------------gtgagccttatgtcactaatacatatcatac-tccacttcctgagtcttactgtttttggctgattattcgttcat-----atgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------------tgttgattgatgc-atgtaagtgactccacctagtggggtaaggtgtgggtttttttagt-------tgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
                                                           | |  | |  | | |   ||||   |   | |        |   | ||  ||||||||         | |  || |||  | ||  | |    | | | ||  |||||||||||| ||||| || || ||||| ||||||||||| |||||  ||||||||||    || || ||||| ||||| ||||| ||||||||||
gtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtg-gctatgtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCAGAATCCGTGTTCTTCATCATTATCTGCTTGCTATGCAAAAAG

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|15203210|gb|BI425978.1|BI425978
EST:     TCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT                         TGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCA
genomic: TCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtaagtgttt ... cttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCA
EST: gi|23727557|gb|BU761813.1|BU761813
EST:     TCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT                         TGGCTGCTCACCTTACTGGGATACACAGTGCCATCAAAATGCTTCATAGCA
genomic: TCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtaagtgttt ... cttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG
                                            tcttaat  putative branch site (score: 3)
                                  ttccatgttttctt  CT-rich tract
     ttttttagttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG

tgttgat
- - - - - -gcatgta
- - - - - - - - - - - -ctccacc
- - - - - - - - - - - - - - - - gtggggt
- - - - - - - - - - - - - - - - - - - - - gtgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt