Sequence
atgc intronic sequence ATGC exonic sequence...gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
Basic information
species | Glycine max |
transcript | GLYMA12G20180.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
---------------------------gaggttattgattgtggggatggggattttgggttttg--gaactgatggggcttttctt-----tttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
||| | || | ||| | || ||| | || | | || || || ||| | |||| ||| ||| | |||| || ||||| || ||||| ||||||||||| || |||||||||||||||||||| || || || | |||||||| ||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgttt---ttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
---------------------------gaggttattgattgtggg---gatggggattttg-ggttttggaactgatggggcttttctttttttcttttc-ttgaactttttttgtg-gtttgtgt-tttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| | ||||||| || | | | || || | | || || | | || | | || | | || ||| |||| || ||||| | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
--------------------gaggttattgattgtggggatggggattttgggttt-tggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttt-tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
|| | |||| | | || | | |||| | | | || || | | | | || |||| ||| | | | | ||| | ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
------------------gaggttattgattgtggggatggggattttgggttt-tggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttt-tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
|| | |||| | | || | | |||| | | | || || | | | | || |||| ||| | | | | ||| | ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
gtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
-----gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
||| | | || | || || ||| || | ||| || ||| | ||| | | | | | |||| || | | | |||||||||||||||||||||||| || ||||||||||| |||||||| || || |||| |||||||| ||
gtacggagctcctcaatcctttcattgttgactttttcttct----ctgtgcatgcgttttgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
-----gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
|| | | | | || | | | |||| |||| || ||| | || ||| | ||| || | | ||| | | |||||||||||||||||||||||| || ||||| ||||| |||||||| || || || | |||||| | ||
gtatgaagctcctcaacccttccattgctggctgtccctttt---actgtgcatgcatttttagcttgcttgtgatgattgggttgtctatttt---ctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
--gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
|| || || || | | | || | | || ||| | | ||| || ||| | |||| ||| || | |||||||| ||||||||||| |||||||| || || || ||||||||||| || |||||||| ||||| || ||
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatct--gttgtgggttgttgttggt--tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gaggttattgattgtggggatgggg-attttg--ggttttggaactgatgg--ggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
||| | || | ||||| || || | ||||| | | | || | ||| | ||| | || || || ||| |||||||||||||||||| ||||||||||||||||| |||||||| ||||| || || || ||||||||||| ||
-------------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttt-tgtggtttg--tgttttgaa--gGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
||| || | | | ||| ||| | || | |||| | | | ||| | ||| ||| | || |||| || | ||||||| |||||||||||||||||||| || |||||| | ||||| |||||||| ||||| |||||
-----tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttt---tttcttttcttgaactttttttgt---ggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| | ||| ||| | ||| || | |||| || | ||| | |||||| | ||||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || ||
-----------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgcggaa-acagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttt-tttcttttcttgaacttttttt--gtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| ||| ||| | | ||| | |||| | || | ||| | |||||| ||||| | || | | ||| | |||||||||||||||||||||||||| || || ||||| ||| | ||||| || || || |||||||||||
-gtctcgttg--tgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
upper sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttt---tttcttttcttgaactttttttgtggtttgtgttttgaa--gGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| | ||| ||| | ||| || | |||| || | ||| | ||| |||| || |||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || ||
-----------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctcttttt---ttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGMapped 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|31464371|gb|CD406399.1|CD406399EST: TTCGAGTACAAGGCCGCCACCGGGGCTTTCACCCCTGACCGTGTTGCTGT GTATTGC-AATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
genomic: TTCGAGTACAAGGCCGCCACCGGGGCTTTCACCCCTGACCGTGTTGCTGTgtgagttttt ... tgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
EST:
gi|20075995|gb|BQ094778.1|BQ094778EST: TTCGAGTACAAGGCCGCCACCGGGGCTTTCACCCCTGACCGTGTTGCTGT GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
genomic: TTCGAGTACAAGGCCGCCACCGGGGCTTTCACCCCTGACCGTGTTGCTGTgtgagttttt ... tgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
ttttctttttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
- - - - -gattgtg
- - - - - - - - -ggatggg
- - - - - - - - - gatgggg
- - - - - - - - - - - - - - - -ggttttg