Sequence
atgc intronic sequence ATGC exonic sequence...tttgactttgaaattattgatcctacaaatggtgtactgtacctcagttttagattttaatctcatgatgattggtcttgttttcaacaatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
Basic information
species | Glycine max |
transcript | GLYMA14G12420.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G106056_T03 (Zea mays), 3'ss of exon 8
tttgactttg-aaattattgatcctacaaatggtgtactgtacctcagttttagattttaatctca--tgatgattggtcttgttttcaac-aatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
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gtaggtgtagcaaattaaacaacaaagggaaacagtttgttcaattgtttttggaccttcattttggttaatgaaaag-caaatctacaactgaactcttgcagGATAAAGACAAACCCTAAAAGTGCCATCAATGAGCATTTCTTACCACGTTTCCTGGATTTTATTGTATGGGGCCATGAGCATGAATGTCTTATTGATCCT
upper sequence: GLYMA14G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 8
tttgactttgaaattattgatcctacaaatggtgtactgtacctcagttttagattttaatctcatgatgattggtcttgttttcaacaatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
|||| |||| | ||| | | | || | ||| | | ||| | ||| | ||| |||| ||| || ||||| ||| ||| || |||||||| |||| ||||||||| | ||| | ||||| |||||||||||||||||||||||||||||||| | | |||||
------gttgattccattgctataacatcttttagatcgttttcttactc---attctg-tatcagaaaatttgatactgtattcat--atgacttgcagGGTGAAATCAAACCCCAAAAATGCAATAAGTGAGCACTTTCTTCCACGTTTCCTCGACTTCATTGTGTGGGGCCATGAGCATGAATGCCTAATCGACCCC
upper sequence: GLYMA14G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g03680.t01 (Vitis vinifera), 3'ss of exon 7
tttgactttgaaattattgatcctacaaatggtgtactgtacc----tcagttttagattttaatctcatg--atgattggtcttgttttcaacaatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
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-----tcttgtacttcttt-ttctatcaatatatctttgtgtcgttttcaatcaaaaaaaaaaaaggtatgcgataatcaaacttaacttctttcatggtctgcagAGTAAAGACAAATCCTAAAAATGCAATCAGTGAGCATTTTTTACCAAGGTTCCTAGACTTCATAGTGTGGGGGCATGAACATGAATGTCTTGTTGATCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttagattttaatctcatgatgattggtcttgttttcaacaatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
ttttaat putative branch site (score: 3)
tagattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgactttgaaattattgatcctacaaatggtgtactgtacctcagttttagattttaatctcatgatgattggtcttgttttcaacaatggtatgtagGGTTAAAATAAATCCAAAAAATGCGATAAATGAGCACTTCTTGCCATGCTTCCTAGACTTCATTGTGTGGGGCCATGAGCATGAATGTTTGGTTGACCCG
- -gactttg
- - - - - - - - - - tcctaca
- - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - ctgtacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga