Sequence
atgc intronic sequence ATGC exonic sequencegtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
Basic information
species | Glycine max |
transcript | GLYMA16G15820.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 7
gtcagagtgtcccctcaatagatggactttgttgttctttgag----aattaaggagatg-ttagtctcatcatcgcagttttgta-attgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | | | |||| |||||| | | || | || | ||| ||| | || | ||| | | || || |||| || || ||||||||| | | || ||||| | |||||||||||||||||||| |||||||||||||| ||||||| ||||| | || ||||||
gttggcat---tctccaatgcgcttgttttgtttatacataaggttaactttacatcatgattaacttgatggttgcattatattatatgacagGTGGACGAGAATTTTCTTATGAGGACATTTGGTCGTTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTCGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
| | | || || ||| | | | || | | | | | | | || | | | | ||||| ||||| ||||||||| | | || ||||| | |||||||||||||||||||| |||||||||||||| |||||||| ||||| | || ||||||
-------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 7
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
| | | || || ||| | | | || || | | | | | | || | | | | ||||| ||||| ||||||||| | | || ||||| | |||||||||||||||||||| |||||||||||||| |||||||| ||||| | || ||||||
-------------gttgctttctctgctgtgcggtttagttaaacttgtatgcattgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaatt--gtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | | | | ||| | | | |||| | ||| | || || | | | |||| | | |||||||||||| ||||| ||||| || ||||| ||||||||||| || || |||||||| ||||||||||||||||||||||| ||||||| ||||| ||||
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggt-ataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10800.1 (Arabidopsis thaliana), 3'ss of exon 6
----gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcat-catcgcagttttgtaat----------tgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | | | |||| || | ||||| | | | | | || || || || | | | | | |||||| | | ||||||||||||||||||||||| || ||||||||||||||||| || || |||||||| || |||||||||||||||||||||||||||| |||||| |||
gtttgttctcatccaacttaaatacctg--cgttgttttccatagctatatatcataattttcttcccttgcctaaaacttttgtggtattgtctttttttagGTTGATGAAAATTTTCTTCTGCGGACTTTTGGAAGATTTGGGCCAATAGCTAGTGTTAAAATTATGTGGCCAAGAACAGAGGAGGAGAAAAGGCGAGAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
| | | || | | |||| || |||||| | || | | || ||| ||| | || ||||| ||||| ||||| ||| | |||||||||||||||||||| ||||| ||||||||||| || |||||||| || ||||| ||||| | ||||| ||||
gttgcattcctaatttttggatgctcaattctctgttattcttttactctttaatgctctttggacctgaaaccaacaaaa----tataatctgtttttattttttatagGTGGATGAGAATTTCCTTTTGCGTACTTTTGGAAGATTTGGTCCTATCGCTAGTGTGAAAATAATGTGGCCTAGGACAGAAGAGGAACGGAGGCGACAAA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 6
-------gtcaga-gtgtcccctcaatagatggactttgttgt----tctttgagaattaaggagatgttagtctcatcatcgca-gttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | | | | | ||| | | || || | | || | || | | ||| ||| | | ||||| | |||||||||| || ||||| | | |||||||| ||||||| |||||||| ||||| || ||||||||||| || ||||| || ||| | ||||||||
tcctctagttatacattttttggtagtagtttggtttaaggaaaatgtccacatctgtcacggttgtcgtacttttctcagagcatatatcgtaat-gcagGTTGATGAGAACTTTCTGTTGAGAACTTTTGGGCGATTTGGGCCTATTGCCAGTGTAAAAATTATGTGGCCGAGGACAGATGAAGAGCGCAGGCGGCAGC
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gtcagagtgtcccct--caatagatggactttgttgttctttgagaattaaggag--atgttagtctcatcatcgcagttt-tgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| |||| | | | ||| | | | || | || | || ||| | | | | | || | ||| || ||||||||||||| |||||||| | ||||||||| ||||||| ||||| || ||||| || || ||||||||||| ||||| || ||| | ||||||||
tctcctcttgtagcgtgttgtttagtggtggttggtacagggactagtatgtgccttcaatgactatattactattctgaggggagctaatgtggtt-cagGTTGATGAAAACTTTCTTCTGAGAACTTTTGGACGATTTGGGCCTATCGCCAGTGTAAAAATCATGTGGCCAAGGACAGATGAAGAGCGCAGGCGGCAGC
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ32251 (Selaginella moellendorffii), 3'ss of exon 5
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | || |||| | | | || || | | | || | | || |||| |||||||| || || || | || || || | |||||||| ||||| || || ||||||||||||||| ||||||| ||||| ||||| ||||
-----------------gtaaagcttctatgttttctcgttctctctcttgatatatatatatatatat----atgcactggtttcagGTCGATGAAAACTTCCTGCTGAGGACGTTCGGTCGTTTTGGACCAATTGCCAGCGTCAAGATTATGTGGCCACGAACAGAAGAGGAAAGAAGAAGGCAGC
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16538 (Selaginella moellendorffii), 3'ss of exon 5
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
|| | || |||| | | | || || | | | || | || |||| || ||||| || || || | || || || | |||||||| ||||| || || ||||||||||||||| ||||||| ||||| ||||| ||||
-----------------gtaaagcttctatgttttctcgttctctctcttgatatatatatatatgcactg----------gtttcagGTCGACGAAAACTTCCTGCTGAGGACGTTCGGTCGTTTTGGACCAATTGCCAGCGTCAAGATTATGTGGCCACGAACAGAAGAGGAAAGAAGAAGGCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
ttttgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA