Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
Basic information
species | Glycine max |
transcript | GLYMA03G40290.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctg-atatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| | | | | | | ||| || | |||| || || ||| | | | | | | |||||| | ||| | |||||||||||||||||||||| ||||||| ||| || || ||||| ||||| ||||||||||||||||| || ||||| || || |||||||
-----------------ttggcagtctgtaatttctttaatctcactttgcaccagcatcttccaaagtacatgatattgatattttttttgaccctttcatatatatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gtaagttttaaagaacttcagaaatgt-tctgtacagtatgtcttttttgagctctatatcta-ttttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
||| || | | | | | | | | | || || ||| | || | || | | | || ||| |||||| |||||| || |||| ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || |
-----------------------gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtt-tgatat---tggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctat-atctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
||||| | | || | | | || | || | ||||||| | | | ||| ||| |||| | || | || |||||| ||| | | | |||||| || ||||||| ||||| || || ||||||||||| ||||| ||||| || ||||| ||||||||||| || ||||| || || | || ||||
gtaagcaccctgtactattagca---tcatatagatcctg-cagatttgagcaatgtcagctaaatttaattgtaatggataatctgat-attaacctgtttctttttgtg--gcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 9
gtaagttttaaagaacttcagaaatgttctgtacagtatgt-cttttttgagctctatatctattttttgt------tgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
|| || ||| || ||| || | |||| | | | | ||||| || ||| ||| | ||| |||| | | | | ||| | | | | |||||||| ||||| ||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || || || || | || ||||
--------------------cttat-ttttgtgtagcatgcactgatctgagttttctgttatccttttgcaaacaacatgataccaagatttgtttctaatattttct--tccaattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatat----tctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
|| || || | || || | || ||||| ||| || | | | | | |||| |||||| | ||||| | |||||||||||||||| || ||||||||||| || || || ||||| ||||| || ||||| |||||||| |||||||| ||| | || ||||
----------------------------gtgcacctctgatcagatgtggcaagggaattcacgctt-gttgtcttactctcttaactgactct---gttcatatatatggcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G311165_T01 (Zea mays), 3'ss of exon 8
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttga-gctctatatctattttttgttgtggta-cattcattaatcattaacgggtt-ctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| |||||| | || | || | | || | || | || | | | | | ||||||||||| || | |||| | |||| || ||||||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || ||||| | || ||||
-------------------gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgta-agTTGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttga-gctctatatctattttttgttgtggtacat-tcattaatcattaacgggtt-ctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA-
| |||||| | || | || | | || | || | || | | | | | ||||||||||| || | |||| | |||| || ||||||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || ||||| | || ||||
-------------------gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgta-agttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
gtaag----ttttaaagaacttcagaaatgttctgtacagtat-gtctttt----ttgagctctatatctattttttgttgtgg-tacattcattaat-----------cattaacgg--gttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
||||| ||| || ||| | | | ||| | | | |||| || ||||| | ||| || || || | || || || | | |||| | | || | | | |||||| ||| ||| |||||||||||||||| ||||| |||||||||||||| ||||| ||||| || ||||| ||||| || ||||| || ||| | |||||||
gtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgttctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggt-tgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------gtaagtt--ttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatcta--ttttttg---ttgtggtacattcattaatcattaacgggttctgatatattc--tgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| |||| || || || ||||||| | | | || || | | | | | ||| | | | | | | ||| | | || | | |||| ||||| | | || ||||||| ||||| ||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||||| ||||
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgt---tgtggtacattcattaatc--attaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| ||| | || || | || | | | | || | || || |||| | || | |||| ||| | | || || | || | ||||| | | || ||||||| || ||| | || ||||| ||||| ||||| ||||||||||| |||||||||||||| || || | || ||| || ||||
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcat-tggtgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| || | | || | | | | | | || || | | | | || | ||| | | || |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || ||||
--------------------------------------------------gtgatagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatgc-cattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA
upper sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
| ||| | | | ||| | | | || | | | | | | | | | || || | ||| | | || |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || ||||
--------------------------------------------gtgagagtttt-tttctgtatagagaggtagcatttcttcttgttctcat--gcgtatgccat----tccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
attcattaatcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT