Sequence
atgc intronic sequence ATGC exonic sequence...tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
Basic information
species | Glycine max |
transcript | GLYMA08G09140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g52390.1 (Oryza sativa), 3'ss of exon 1
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttggtatgtaattccttgttaatg--tagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
|| | | || |||||| || ||| | || | | ||| || ||||| | | | || || || | |||| | | ||||| ||||| | | ||||| |||||||| ||||||||||| || || ||||| | ||| |||||||| || ||||| |||||||| ||||| ||| | |
atttgtagggcatgaaaaaactggatg--tttatactgttctaattgaagtaactgagctggtaaatcagtaatttgtattgactgtttttccttaatacagAAGTTTTCGTCGCTTTTGCTACTGCGGCTTGCATTTCAGAGCCTGGGGGTGGTCTTTGGTGACTTGGGTACATCACCATTGTATGTGTTCTATAATGCCT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g38960.4 (Oryza sativa), 3'ss of exon 2
--tgccatacaaatta-cagaatatggatgcattaataagctattatg--taagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
| ||||| ||| | ||| ||| | | || | | | | | | | | | | || | || || | || | || | |||| | | || || | || || || |||||||| || || || ||||||||||| | ||||||||| ||||| ||||| | |||||||||||||||| |
cctaggatacattttaatggcatacagattc--tgattttttttcacgaatggaccattgaagtattcttgctaactgttcttccc-caattcct--ttatgcagACCTATCCAACAATTTTACTGCTACGGCTAGCTTTCCAAAGCCTTGGTGTGGTATTTGGAGACTTAGGCACATCACCTCTATATGTTTTCTACAATATCT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G327234_T01 (Zea mays), 3'ss of exon 1
tgccatacaaattacag-aatatggatgcat--taataagctattatgtaagctaagggatt---tggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
| ||||| | | |||| | | || || | | || |||| || |||| | |||| || | | | | |||| | | | ||||| || ||| || ||| | || ||||| ||||||||||| ||||| ||||| | ||| ||||||||||| ||||| |||||||| ||||| |||| ||
------agaaatttctctggtttggaagaagaatactagtttttgatttaagtaaatagattgctaaatcaagaatttctgttgactctggtttcttttcttgcagAAGTTCTCATCAGCTTTGTTACTACGGCTGGCATTTCAGAGCCTTGGGGTGGTCTTTGGTGACTTGGGCACGTCACCTTTGTATGTGTTCTATAATATAT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G009353_T01 (Zea mays), 3'ss of exon 1
-tgccatacaaattacagaatatgg---atgcattaataagctatta--tgtaagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
||||| | | | ||| ||| | | || | ||| ||| || || | | | || | |||| |||| | | ||||||||||| || | ||| | |||||||| || ||||| |||||||| || || | ||| ||||| || || ||||| ||||||||||||||||||| |
gtgccacaacagctgtgctccatgtctcatgtactgctagacctttaactgtgtccttagcaaaaaaagactaacttgatctttaaa------tttgttcatgcagAAATTTTCGTCAATTTTGTTACTGCGGCTCGCGTTTCAAAGTCTTGGGGTAGTGTTTGGGGACTTAGGTACATCACCATTGTATGTTTTCTACAATATCT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G005040_T01 (Zea mays), 3'ss of exon 1
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatt---tggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
| || | | | | | | ||| | | || |||| || |||| || ||| || | | ||| |||| | || ||||| || ||| || ||| | || ||| | ||||||||||| ||||| ||||| | ||| ||||||||||| ||||| || ||||| ||||| |||| ||
---agaagaatctccggttcagaagaagaatcatagtttgtgatttaagtaaatagattgctaaataaaaaatatctgctgactgttgtttcctttcgtgcagAAGTTCTCATCAGCTTTGTTACTACGGTTGGCATTTCAGAGCCTTGGGGTGGTCTTTGGTGACTTGGGCACGTCACCTTTATATGTGTTCTATAATATAT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g01510.t01 (Vitis vinifera), 3'ss of exon 1
----tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
||| || | || | | | | | | | | || | || | | | || | | | || | | | ||| | |||||||| || ||| | |||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| || ||||| ||||||||||| |||||||
tgaatgctcaacctaatagaaggtgagagaccgtgaggatattgttgt-ta---ttggtgcttcaaatttgatctgtatgctgagtcattttgattccatgcagAAATTCTCGGCAGTATTGCTTCTTCGGCTTGCATTTCAGAGTCTTGGAGTGGTCTATGGAGACTTGGGCACATCTCCCTTATATGTTTTCTATAATACAT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S96_141V6.1 (Physcomitrella patens), 3'ss of exon 1
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttgg---tatgtaattccttgttaatgtagtttttggt-tgtt-cagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
||| | | | | | | || | ||||| || | | | ||| || || | | | || | ||| | || | | | | ||| ||||||| |||||| || || || || |||||||| |||||||| ||||| |||||||||||| | | |||||
-----cgtcgattccgtaggttaacaagttcggtgttcggttctctaagccaaatcttccacaccttcttggaatcttaacaaaaattttctcgatgtgctgcagGCAGTTACGCTAGGTGCGATAATGCACCTAGCATATCAGAGCCTAGGGGTAGTCTATGGAGATTTGGGCACATCACCATTGTATGTTTTCAAGAGTACAT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S143_101V6.1 (Physcomitrella patens), 3'ss of exon 1
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttg----gtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTT---GCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
| || | | | | | | | ||| | || | |||| ||| || | || | || |||| ||| | | | | | || | | |||| ||||||| |||||| ||||| ||||| ||||||||||||||||| ||||| |||||||| ||| | | || |
-------tctactagaccttgttgccgttgtgacaaggttcagagtcgatttagggtcttgcagaaaattttgttttgtaacaagactgtttccttgtgtgttgcagGCTGTATCTCTGACTACGGTGTTGCGTCTAGCATATCAGAGCCTTGGGGTGGTCTATGGAGACTTGGGCACATCACCATTGTATGTATTCAAGAGCACTT
upper sequence: GLYMA08G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S118_70V6.1 (Physcomitrella patens), 3'ss of exon 1
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttggtatg---taattccttgttaatgtagtttttggttgttcagAAATTTT--CAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
| | | | | | || || | || | || || |||| || | ||| | | |||| |||||||| | | | | | | | || | || | ||||| |||||||| ||||| ||||| || |||||||||||||| ||||| |||||||||||| | | || |
-----ctccagtaggacatgcttgacattgtagtgagggaaagagttgacttagggcttccgaatgacttgggtgacctaacatgtggtttttggggccttgtagACTATGCCTCCGAGTGTGGTGTTGTGCCTAGCGTTTCAGAGCCTTGGGGTGGTCTACGGAGACTTGGGCACATCACCGTTGTATGTTTTCAAGAGCACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
tgttaat putative branch site (score: 3)
ttaatgtagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgccatacaaattacagaatatggatgcattaataagctattatgtaagctaagggatttggtatgtaattccttgttaatgtagtttttggttgttcagAAATTTTCAGCATTGTTGCTTCTGCGGCTAGCATTTCAGAGTCTTGGTGTGGTTTATGGAGACTTGGGCACTTCACCCTTGTATGTTTTCTACAATACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- ccataca
- - - - - - - - - - - ggatgca
- - - - - - - - - - - - - - - - - - - - - -tgtaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtag