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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactgcctggcggccatcccctcacactccacccccttttccttttgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

Basic information

species Glycine max
transcript GLYMA06G03070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------cactgcct--ggcggccatcccctcacactcc-acccccttttccttttgcagcaattctttgaaaaagatcctgaatgaacttgtg-accttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
|| || | | | ||| | | | || | ||| | || | | || ||| | || | | | || |||||||||| |||| ||||||||||| || || ||| ||||||| ||| |||| | || || ||||| | ||||| ||||||||||||||||||||| |
gtatattcttgatttatttggcgtctctatttttaagtgaaaaaaacattggttaagatactttatttgtggtgttcctatgaacaacaaatattttattcattactctcaatggttgctttgtgattgtttgtgcttcgttttatgcagCAATTCCTGAAGGAGATTCTGAATGATCTGTGTTTTTACAACAAACGAGGACCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCTACAG

upper sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G060284_T01 (Zea mays), 3'ss of exon 5
-cactgcctggcggccatcccctcacactccacccccttttcctt----ttgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
| | ||| | | ||| | | || || || | | | | | | | || || | | | | ||| | |||||||||| |||| ||||| ||||||| || ||||| || |||||| ||||| | || || ||||| | ||||| |||||||||||||||||||| |
gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG

upper sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 5
---cactgcctggcggccatcccctcac-actccacccccttttccttttgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
||| || || | | || || | | || | |||| | | || |||| | | | || || ||||||||| ||||||||||| |||||||| || || || |||||||||||||| |||||||||||||||| ||||| ||||| || || |||||||||| ||
tctttttgcttgcttatcacaaaataattacatggtgtactagtattctttgattggatcttc--acctggtcaggaatt--ttgggtgtttctttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGAACCAATCAAGGAACTTATGAGCTTAAGCCAGAATATAAGAAATCTGCTG

upper sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S149_261V6.1 (Physcomitrella patens), 3'ss of exon 5
cactgcctggcggccatcccctcacactccacccccttttccttttgcagcaatt--ctttgaaaaagatcctgaatgaacttgtgaccttttcttt---cgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
| | || | | | | | | || | | || || || | |||| | ||| || | |||| || ||||||| || ||||| || || || | ||||| |||||||| || |||||||| || || ||||||||||| ||||||||| | |
-----gcggtggggaaaggaggtggatgatttgttggtatgggtgggaagtgggtgacacagagaagcatgcaagatgagttggtggtggttgtggtgtgtgcagGCGTTTCTGAAAGAAATACTGAATGACCTGTGCATCTACAACAAAAGAGGCGCGAATCAAGGGACGTATGAGCTGAAGCCAGAGTACAAGCGGACCGAGA

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|58023918|gb|CX710659.1|CX710659
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|192294408|gb|FG987337.1|FG987337
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|193393205|gb|FK358441.1|FK358441
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGT
EST: gi|37994152|gb|CF805898.1|CF805898
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|151398032|gb|EV267910.1|EV267910
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAG
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAG
EST: gi|23735091|gb|BU765812.1|BU765812
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|58024109|gb|CX710850.1|CX710850
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|19345950|gb|BM890830.1|BM890830
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|192300028|gb|FG991846.1|FG991846
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAG-T
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|8825687|gb|BE209480.1|BE209480
EST:     AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgctttt ... tctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
                                        ccttttctttcgc  CT-rich tract
 aattctttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactgcctggcggccatcccctcacactccacccccttttccttttgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
cactgcc
- - - -tggcggc
- - - - - - - - tcccctc
- - - - - - - - - - - - - ctccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgacc