Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
Basic information
species | Glycine max |
transcript | GLYMA19G42900.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
--gtaagttttaaagaacttcagaaatattttgtag-agtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| ||| | || ||| | | |||| | || || | | | |||| || |||| || | || |||| || | || ||| | |||||||||||||||| ||||| ||||||| ||| || || ||||| ||||| ||||||||||||||||| || ||||| || || |||||||
ttggcagtctgtaatttctttaatctcactttgcaccagcatcttccaaagtacatgatattgatatttttttt------gaccctttcatatatatatattt--cagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctat-atctattttttcttgtgaaagg-gttctgatat--atctacaagttct----gcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
||||| | | || || | |||| || ||||||| | | | ||| ||| |||| | | |||||||| | || || | |||||| || ||||||| |||||||| || ||||||||||| ||||| ||||| || ||||| ||||||||||| || ||||| || || | || ||||
gtaagcaccctgtactattag---catcatatagatcctgcagatttgagcaatgtcagctaaatttaattgtaatggataatctgatattaacctgtttctttttgtggcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggt-tctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| | || | ||| | ||||| |||| | || | ||||| | | ||| | | | | | | | | |||||| || |||| |||||||| || |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || |
----------gtgtgcctctgc----tttgatgcagtatcaaaatttgca-tatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 9
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| | |||| | | | | | | | || | ||| | | | | | | | | || | |||| |||| | | | ||| | | | | |||||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || || || || | || ||||
cttatttttgtgtagcat--gcactgatctgagttttctgttatcct---tttgcaaacaacatgataccaagatttgtttctaatattttcttccaattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgat-atatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| || || || | | | | | || ||| | ||| | | |||| || | |||| | |||| || | ||||| | ||||||||||||||||||| ||||||||||| || || || ||||| ||||| || ||||| |||||||| |||||||| ||| | || ||||
----------gtgcacctctga----tcagatgtggcaagggaattcacgcttgttgtct-tactctctt---aactgactctgttcatatatatggcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G311165_T01 (Zea mays), 3'ss of exon 8
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctc--tatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
|| || | || | | | | |||| | ||| || | || || | || ||||| | | | ||||| | || ||||||||||||| ||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || ||||| | || ||||
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagTTGCTCGATT--------TGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctc--tatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA-
|| || | || | | | | |||| | ||| || | || || | || ||||| | | | ||||| | || ||||||||||||| ||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || ||||| | || ||||
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatt--------tgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
------------gtaagttttaaagaacttcagaaa----tattttgta--------gagtatgtctttttgagctc---------tatatctattttttcttgtgaaagggtt-ctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
||| || | | ||||| | || | || |||| | ||| ||| || |||||| || ||| || || | || | | || |||||| ||| ||| ||||||||||||| || ||||| |||||||||||||| ||||| ||||| || ||||| ||||| || ||||| || ||| | |||||||
gtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgt-tctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------gtaagtt--ttaaagaacttcagaaatattttgtagagtatgtctttttgagctc-----------tatatctattttttcttgtgaaagggttctgatatat-ctacaagttc------tgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| |||| || || || | || || | | | || |||| ||| | || ||| || | | || | | ||| ||||| | | || ||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||||| ||||
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------gtaagttttaaagaacttca-----gaaat-attttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| || |||| || | || ||||| | | | | || | | || |||| ||| | | | | | || || | ||||| | | || ||||||| || || | || ||||| ||||| ||||| ||||||||||| |||||||||||||| || || | || ||| || ||||
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcat-tggtgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
|| | |||| | | | || |||||| | ||||| || | | | | | ||| | | || |||||||| || || || || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || ||||
--------------------------------gtgatagtttttttctgtatagagaggtagcatttcttctt-----gttctcatgcgtatgccattc---cagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
|| ||| | | ||| || | | | || |||||| | ||||| || | | | | | ||| | | || |||||||| || || || || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || ||||
------------------------------gt-gagagtttttttctgta-tagagaggtagcatttcttctt-----gttctcatgcgtatgccattc---cagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
ttctgat putative branch site (score: 3)
tatctattttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT