Sequence
atgc intronic sequence ATGC exonic sequence...caacacatcattttctttagatggcattgcacatttgctgtactatgagcaatgaagtatattatttcctactgtatgctgatgctataatcttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
Basic information
species | Glycine max |
transcript | GLYMA16G26140.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034833_T02 (Zea mays), 3'ss of exon 2
-caacacatcattttctttagatggcattgcacatttgctgtactatgagcaatgaagtatattatttcctactgtatgctgatgctataatcttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
||||| ||| |||| || | | | | | | || ||| || | ||| | | ||| ||| ||| | |||||| | |||| ||||| |||| || || || || || ||||||||||||||||||||||| ||||| ||||| | | | ||| |
cgtacacaa-attatcttcagtcatggtcgtgctggtaaagagaagaaaacagagaatgatcatcccatctaacttgtttacgcattatgccacctttcagGATCTGAGTCTTCTGCTTCTAACTTCTGGGAGAGATCCGGGGATCATACCTCGCAATGCACATCCTCCAGAACCTGAAGGGTTTGATGACAATGCAGAGG
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 2
caacacatcatttt-ctttagatggcattgcacatttgctg-tactatgagca-atgaagtatattatttcctactgtatgctgatgctataatcttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
| |||| | |||| || | ||||| || || | || | | || || ||| | | ||| ||| ||| | |||||| | |||| ||||| |||| || || || || || ||||||||||||||||||||||| ||||| ||||| || | | ||| |
--atacataaaaaaattttatctgaagtcatgatcatgctggtaaagagaatatatacaaaacataccctctaact-tgtttaagcattatgccacctttcagGATCTGAGTCTTCTGCTTCTAACTTCTGGGAGAGATCCAGGGATCATACCTCGCAATGCACATCCTCCAGAACCCGAAGGGTTTGATGGCAATGCAGAGG
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
caacacatcattttctttagatggcat-tgcacatttgctgtactatgagcaatgaagtatattat--ttcctactgtatgctgat-gctataatc--ttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
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------atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagcaatgaagtatattatttcctactgtatgctgatgctataatcttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
tgctgat putative branch site (score: 3)
tctttttt putative PPT
aatgaagtatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacacatcattttctttagatggcattgcacatttgctgtactatgagcaatgaagtatattatttcctactgtatgctgatgctataatcttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-aacacat
- - - - - - - - - - - - - -tgcacat
- - - - - - - - - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - - - - ctatgag
- - - - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcta