Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactaatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttgtatgtataatgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG

Basic information

species Arabidopsis thaliana
transcript AT5G37510.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 2
---gttactaatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcct--gttgattag--gttttgtatgtataatgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
   ||  ||  |||  | |  |   |     |  | ||   |       |    | |||| |||  |  | || |    ||||||| | |       | | ||||| ||  ||||||||  ||| |||||||| ||||| || || |||||  |||||||||| ||||| || ||||||||||| ||||| || || ||||||
gtggtagct--tatcatcttatatcaaaacaaaatattgtctggctgcttcttcaagctacccttggccggtttgtaactttgtatttcttgaaaaat-gcagGTGCGTCAGATTTGCTAGTGAGGTTGCTGGTGTTCAAGACCTGGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTGGAGAAACTTATG

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 2
-gttac-taatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttgtatgtataatgttt---ttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
  |||| |   || |    | | |  |     ||| |   || |     |    |  |||||||     || ||  ||  | | | || ||    ||| ||||||||| | |||||| |||| |||||||| ||||| || ||||||||  |||||||||| ||||| || ||||||||||| |||||||| || ||||||
tcttacattgcattgacatcatgtgctaaatggttctctctacttgtgcaagctctgtatcctggctgatatgtgatgc-tattttattttcaaattgcagGTGTGTAAGGTTTGCTACTGAGGTTGCTGGAGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 2
gttactaa--tatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttgtatg-tataatgttt---ttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
 ||  |||  | | ||   ||  |  |||       | |||   |  |    | |    | ||||  ||| | |  | | || |   || |||   ||| || |||||  | |||||| |||| |||||||| ||||| || ||||||||  |||||||||| ||||| || ||||||||||| |||||||| || ||||||
-tttttaatttgttgtcatctcgtgctgtagaacaattgttctcgcaacttgtgcaa-gttctgtacattggctgatatgtgatgctatttttaaattgcagATGTGTCAGGTTTGCTACTGAGGTTGCTGGTGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------gttactaa------tatagtttgcttatagtgtgatgttttagtt------aatgtgatagatacgctatcctg-----ttgattaggttttgtatgtataatgttttt-----gtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG-
                                                             ||| |||      || |  |||   ||  | | |||  ||| ||      ||  |   |  |||  ||  |||      |||   || | ||   | ||  |  |||        || |||||  |||||||  | || ||||||||||||||||||||||| ||  |||||||||| ||||||||||| |||||||| ||||||||||| ||| || 
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------gttactaat--atagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctg-----ttgattaggttttgtatgtataatgtttttgt-----agGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
                                                                        |||||  ||    | |    ||||    |  |  ||     ||  |  || ||||  ||  |||      |||   || | ||   | ||  |  |||  |     ||||||||  |||||||  | || ||||||||||||||||||||||| ||  |||||||||| ||||||||||| |||||||| ||||||||||| ||| ||
gtcaatattggactaaactttatttttttccctgtaaatctgattattgtgaatgcagattttattaaacatgttacacattggaaatcatattatgacttatttcttctaaaaacttattaaatactttaatctgagtgcctgaaagggctctggtggaatgtttctttctttcaacagGTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGCAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTG

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
----gttactaatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttg-tatgtataa---tgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
     ||| |   |    ||| ||  || ||  |  | | ||| | |||| || | |   || ||  | |  || ||||| | || | |    || |     ||||||||  | |||||  |||| ||||||||||||||||||||||| ||  | || ||||| || |||||||||||||| |||||||||||||| ||||||
tcacattaatttcaactcttgatttgagagtatttgtctggttta-gtga-agctgcatcattct--ttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG

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|116457684|gb|EG500276.1|EG500276
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         -TGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTC
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTC
EST: gi|116446464|gb|EG489056.1|EG489056
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         GTGTGTACGATTTGCTTCTGAAGTTGCTGGGG
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGG
EST: gi|116411626|gb|EG454218.1|EG454218
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         GTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCACGATCTTGGTATACT
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACT
EST: gi|125296822|gb|EL310907.1|EL310907
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         GTGTGTACGATTTGCTTCTGAA
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAA
EST: gi|125042963|gb|EL115232.1|EL115232
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         GTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGG
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGG
EST: gi|116446466|gb|EG489058.1|EG489058
EST:     CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAG                         GTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACT
genomic: CTTGGTCCTCTTGTGAAGACTGTTATGACTCGGTGTATCCAGTGTACAAGgttactaata ... gtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatagatacgctatcctgttgattaggttttgtatgtataatgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG
                   tgttgat  putative branch site (score: 4)
                                            tgttttt  putative PPT
                              ttttgtatgtataatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactaatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttgtatgtataatgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA