Sequence
atgc intronic sequence ATGC exonic sequence...attagaactctatgtaggatatgtggtatatgagtatattgggtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
Basic information
species | Glycine max |
transcript | GLYMA12G36630.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36630.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
attagaactctatgtaggatatg-tggtatatgagtatattgg-gtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
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--catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
upper sequence: GLYMA12G36630.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G052606_T01 (Zea mays), 3'ss of exon 1
attagaactctatgtaggatatgtggtatatga---gtatattgggtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
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-gtacgtacgtacgcatgacactttctctctgacagaaagatcctggatcgatcgtttgcttactgtgaaa--tcaaccctcacttgcgacattatattccagGTGGTCTCAGATTGCTGCCCGGTTGCCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGGCTCAAGAACAGCTCGGCA
upper sequence: GLYMA12G36630.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
-attagaactctatgtaggatatgtggtatatgagtatattg-ggtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTC-CACATTGAAGAAAAGGTTGAAAACTAACACTTCC
|| ||| | | |||| | || | ||| || ||| || || || || || | || || | || ||||||||| ||||||||| | | ||||| |||||||| ||||| ||||| ||||| ||||||||||| ||| | | ||| | | | ||
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaat--cggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
ctttaat putative branch site (score: 4)
ctttctttcttctctt CT-rich tract
ttctttaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagaactctatgtaggatatgtggtatatgagtatattgggtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - tatgtag
- - - - - - - - - - -tgtggta