Sequence
atgc intronic sequence ATGC exonic sequence...gcttatataatttgtcactgaatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G36570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 3
gcttatataatttgtcactg-aatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttga---------tttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
||||| || ||| | || || || ||| | | | ||| | | | || | || | | ||| ||| ||||||| ||||||||||| ||||| ||||| ||| | || |||||||| |||| ||||||||||||| ||| || ||| | | ||| |||
---------gtttgtatctctaatatgctctgcagattcagttgctgccacttatgtgcatgtt-tcagttgactgttccccttgttacttttggacaaacttctttcagGAAAGTATGTTGGGAATCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGCAAAGACAAAAG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 3
----gcttatataatttgtcactgaatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgt---ctttgact--cttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
| | | |||| ||| | | | | || | | | || | | | || | ||| | |||| ||||| | | ||||||| ||||||||||| || || ||||| ||| | || |||||||| |||| ||||||||||||| ||| || ||||| | ||| |||
gtttgtatctctaatatgttctgcagattcagttgc-tggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------gcttatataatttgtcactgaatcttgtcaacatatgcagca-gacaatatagtagaa--aatgctgtaaaatgtgt--attttgtct-ttgactcttgat-----ttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
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gtaagcaccttgtttttagtttctgtttgatgtgttgcttcatcttgatatctcatctcactgt-ttttgtcagaacttgttatatgattctgttctataatcactgtcgttgaacattctgatttggtccactgatttcatatgaatacacagGTAAGTATGTTGGAAATCGTCCGATAAAACTACGAAAGAGTAGCTGGAAAGAGAGAACAGATCAGGAGGCTGCTGAAAGACAAAAG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 4
-gcttata-taatttgtcactgaatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
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aggttatggtggctcattataatgactagtaaa-gtttg-agcattgagaaaagttttggatataatggcttaaatatgttgatttaaatctcaattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 4
--gcttatataatttgtcactgaatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
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acgatgctgaaggttataa-tgacttaaaataacaagttttaatgttgaga-agtttctgctataatgacttacgtatgttgatttaaatctcaattttcagGAAAATATGTTGGAAATAGGCCAATCAAACTACGTAAGAGCAATTGGAGGGAGAGGACAGATTTTGAAGCCTTGGAAAGACAAAAGMapped 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|193601564|gb|FK549455.1|FK549455EST: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST:
gi|31462737|gb|CD404765.1|CD404765EST: GAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATG GTAAGTATGTTGGAAATCGTCCTATAAAACTACGCCAAGAGTAAGTGGAGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACG-CAAGAGTAAGTGGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
tcttgat putative branch site (score: 4)
ctctt CT-rich tract
taaaatgtgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttatataatttgtcactgaatcttgtcaacatatgcagcagacaatatagtagaaaatgctgtaaaatgtgtattttgtctttgactcttgatttcagGTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - -cactgaa
- - - - - - - - - - - -cttgtca
- - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - -gcagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgta