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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggcaaccatttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT

Basic information

species Glycine max
transcript GLYMA19G35990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G175419_T02 (Zea mays), 3'ss of exon 3
----------cacaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatg--------atggccttattgtttctggcaaccatttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
          | |    ||   | |  ||     |||  |  ||||| |      ||||   ||| || |||| |          |   |||||||||| ||||||||||||||||||||||||||  || ||  |||||  ||| | ||| ||  ||
gtgaagggcgcccttggtgtaatcttattgactgttgtaga-tgatgaagttgcaagttaatgtatttgagtacttcgactcacgtcagcttattgtttgtggcaaccatttccgcagAATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT

upper sequence: GLYMA19G35990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 2
cacaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggcaaccatttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
   || ||  |     |||     |   |  ||      | |     ||  |||| ||         |   |||||||||| ||||||||||||||||||||||||||  || ||  |||||  ||| | ||| ||  ||
tgtaatcttattgactgttgtagatgatgaagttgcaagttaatgtatttgagtacttcgactcacgtcagcttattgtttgtggcaaccatttccgcagAATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT
















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|151406157|gb|EV275972.1|EV275972
EST:     TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
genomic: TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattcccc ... atttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
EST: gi|298180260|gb|HO025475.1|HO025475
EST:     TTGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
genomic: TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattcccc ... atttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
EST: gi|7042407|gb|AW472301.1|AW472301
EST:     TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
genomic: TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattcccc ... atttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
EST: gi|298165666|gb|HO008637.1|HO008637
EST:     TCGAGGACATGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
genomic: TCGAGGACACGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattcccc ... atttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttccagtagttaagtaatgatggccttattgtttctggcaaccatttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT
                                           ccatttcc  CT-rich tract
           ttaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggcaaccatttccgcagAATTCGAGGTGTAGATATGAAGAATGATTTTGCCTTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
cacaaac
- - - -tggtgtt
- - - - - - - - - - - - -tgagggg
- - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - -tcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcaacc