Sequence
atgc intronic sequence ATGC exonic sequencegtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatactcgtgaattgctggtaataacttgagaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
Basic information
species | Glycine max |
transcript | GLYMA09G08180.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G039683_T02 (Zea mays), 3'ss of exon 10
gtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatactcgtgaattgctggtaataacttgagaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
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----tttgtggatactg-ctccacaggatggtacataatactcctgttgcattttatcctgt----ttctgaagaagtgc-----ttgttcatattgtcctta---ttatcttttcaGGGTATTGATAGACAAGATGTCCGTATTGTTTGCCACTTCAACTTGCCTAAGTCAATGGAATCCTTCTACCAGGAGTCAGGTCGAGCTGGTCGTGATCAA-
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G039683_T01 (Zea mays), 3'ss of exon 10
gtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatactcgtgaattgctggtaataacttgagaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
| | || || | | | | ||| | | |||| ||||| | | | | | | | | ||| | || | | | | | | ||||| ||||||||| | |||||| | ||||| |||||||||||| | || |||||||||||| | ||||| || |||||||| |||||||||||||||||
-----ttgtggatactg-ctccacaggatggtacataatactcctgttgcattttatcctgt----ttctgaagaagtgc-----ttgttcatattgtcctta---ttatcttttcagGGTATTGATAGACAAGATGTCCGTATTGTTTGCCACTTCAACTTGCCTAAGTCAATGGAATCCTTCTACCAGGAGTCAGGTCGAGCTGGTCGTGATCAAC
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G35740.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatactcgtgaattgctggtaataacttgagacca--aattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
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------------------------------gtaaacaaagattctttctcatgttg-catctgt--ttaattgtgtacttcttatgtactg-tagcatgatgagactactgactttctagGGCATAGATAAGAAGGATGTCAGAATGGTTTGCCATTTTAACATTCCAAAATCAATGGAATCTTTCTATCAAGAGTCTGGTAGAGCAGGTCGGGATCAAT
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 10
gtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatact-cgtgaattgctgg--taataacttg-agaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
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-----------------aatttcaacaagtttggg-atagtttat----tatttcaagttctggggatgttattaagccatatgatatgttaaattaatggctgatggataaaaacttttagGGCATAGACAGAAAGGATGTCAGAATCGTTTGCCACTTCAATATTCCAAAGTCAATGGAAGCATTCTATCAAGAGTCAGGTAGAGCTGGTCGAGATCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatcttcattatactcgtgaattgctggtaataacttgagaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
taataac putative branch site (score: 1)
ttcattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtactacatggtgattttgtattagcttgactaaaatttctgtgatgttttaacatttgtaatcttcattatactcgtgaattgctggtaataacttgagaccaaattaaccagGGCATTGATAGAAAGGATGTCAGAATTGTATGCCACTTCAACATTCCCAAGTCAATGGAAGCATTCTATCAAGAGTCAGGCAGAGCTGGTCGTGATCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT