Sequence
atgc intronic sequence ATGC exonic sequence...aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
Basic information
species | Glycine max |
transcript | GLYMA10G32500.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
aaatccatgattgactttcattttcaatttagttctctctgta-gaattgaa----attttct-tgtctttgtatttgcttcattaattatcttacgaa-atttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
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------acgaattacttggattca-agttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
--aaat-ccatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
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ccatttgttttgtgtggattacatttgttcact-gttttctttatatagtcttaactgtgta----taacgtttactgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaattt---cagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
||| | | |||| | | | | | || ||||| || | || | ||| ||| || | || ||| |||||||||||||| |||||||||||||| || ||||| || |||||||| || ||||||| || ||||| || || | ||| | || || ||||
-tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcat-gtgccc-ttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaatt---ttcttgtctttgtatttgcttcattaattatcttacgaaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
|| | ||| | || ||| | | || |||| || || | | ||||| || | | | | | | | |||||||||||||||||| |||||||||||||| || |||||||| |||||||| || ||||||| |||||||| || || | ||| ||||| || ||||
----tattggcatgccctcaatag-aagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------aaatccatgattgactttcattttcaat----ttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatctt--acgaaattt-cagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
| || ||| | ||| || || || || || |||| ||| | | || || | | | | || ||||| || ||| | | |||||| || || |||||||||||||| ||||| || ||||| || ||||| || || ||||||||||||||||||| || | || | || || ||||
gtcaactccgatcaacctttctttcacgttgtttgatcccctgacttgatttttttgtcgatatttttcattttctcaacagagt--gcagctttttaccatcaattgagttttcaagattattttgaacgctgtgtgcagGTATTTTTCGTATGAGCATTTTTACGTCATATATTGCAAGTTCTGGGAACTAGATTCAGATCATGACTTTTTCATAGACAAGGATGATCTCCTTCGATAT
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
-----aaatccatgattgactttcattttcaattt--agttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
|| | ||| | | || ||| || |||| | || || | | | | | | || | | ||| | | ||| ||| || || |||||||| ||||| ||||| ||||||||||| ||||||||| | ||| | ||||| |||||| | ||||| | || |||| | |||
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgct-aacaaagactataataattgacctttggatacatgtggtgtgcgacg------cagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaaattttcttgtctttgtatttgcttcattaattatcttacgaaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
atcttac putative branch site (score: 3)
attaattatcttacga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - ccatgat
- - - - - - - - - - - - - - - - - - ctctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttca