Sequence
atgc intronic sequence ATGC exonic sequencegtaatagcaaaaaacaacttcagtttaatgaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
Basic information
species | Glycine max |
transcript | GLYMA04G03010.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------------------------gtaatagcaaaaaacaacttcagtttaatgaacgtggtgtatggtgtatggt-gttcatt---aattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
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gtaagtaagaatcttctatggaatatgccatgattgagttgtatgacaataagattacatatgata-catgatatttttttagaactattatattgttttacttaaaacagtaggccattctcattcagttgtgtaactatgtaacagGTATCAGTTTATTCCTCAGCTGATATTCTTGAACAGCTTATTTGGTTACCTTTCACTCCTCATCATTATTAAGTGGTGCACGGGCTCAAAAGCTGACCTT
upper sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
----------------------------------------------gtaatagcaaaaaacaacttcagtttaatgaacgtggtgt----atggtgtatggtgttcat---taattggttttccgatgaggcctca---------gGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
| | | | | | || || || | | || | | || | |||| |||| |||| | | |||| ||||||||||| |||||||| | || ||||| |||||||| |||||||| || || | ||||| ||||| || ||| |||| |||||| | || || ||
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
upper sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
----gtaatagcaaaaaacaacttcagtt-taatgaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
||| | ||| | | || | | | || | | | | | | | || | || ||||| |||||||||||||||||| |||||||| ||| ||||||||||||||||||| ||||||| || ||||| ||| ||||||| || || || || |
gtgagtatt--caattttctgcccttgtcattacgtacttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
upper sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 13
------------------gtaatagcaaaaaacaacttcagtttaatgaacgtggtgtatggtgtatggtgttcattaattggttttccgat-----gaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
| | || | || | | | | | || | |||| | | || || | | ||||| ||||||| ||||||| || |||||||| |||||||||||||||||||| ||| ||||||| || ||||| ||| ||||||| || || || || ||
gtgggttcagttgatattttctgaccatagcgtgctctctctctctccagttccttaaacagtaaaaatcagtcatcatctcagcatctaattttgcgggcttgcagGTTCCAGTTCATTCCCCAAATGATATTCTTGAACAGCTTGTTTGGCTATCTCTCAGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTG
upper sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 13
-----------------gtaatagcaaaaaacaacttcagttta-atgaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
|| | | | ||| || ||| || | ||| || | | | | || || | | | | | | |||||||||| || ||||||||||| ||||| ||||||||| | ||||| || ||||| |||||||||||| | |||||| ||| || || || ||||| ||
tttttcgttctaaatgtgtgtttgtgcttgagttctttagattatattattgtgttgactatta-aggatgcacaatcagcattaatttg-catttcttcagGTACCAATTTGTTCCCCAGATGATATTTTTAAACAGCCTTTTTGGGTACCTTTCTCTCCTCATAATTGTGAAATGGTGCATGGGTTCACAAGCTGATCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
cattaat putative branch site (score: 3)
ttcattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagcaaaaaacaacttcagtttaatgaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA