Sequence
atgc intronic sequence ATGC exonic sequencegtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttatttttaatgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
Basic information
species | Glycine max |
transcript | GLYMA16G28290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 4
gtattcccataatttactaccctgtattttaaaacagaccttgttaattgt-taatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttatttttaatgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
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---------------------------------------tttagtttttgtattgggttttggctctcaaaattctagtcttactg---gtgatattgcaaaat---cttgatgtataacttcaaatattccatcacatt-----ttcagTGACCAGCTACCTGTCAGTACAAAGTTTGATATGCGTAGCGATCCTGGCGTTGTAAGGAATTATGGTCGGCTCTTGCTGGAGATGGCTTCTGCTGTGCCA
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 4
gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttatttttaatgtttaatcggtttcttgt-ttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
||| |||||| ||| | | |||| || | || | | ||||| | |||| | | ||| || | | | | |||||||||||||| || || ||||| || || |||||| | ||||||| ||||| || ||||||||||| | |||||| ||||||||||||| | ||||||
------------------------------------------ctta--tgttaagcttttata----acatctttagttgtttccaacat--ttcatattactggtagcattgtacactgtgtaaacaccaaccattccatcatcttcagTGATCAGCTACCTGTGAGTACAAAGTTCGATATGCGTAGTGATCCTGGTGTTGTGAGGAATTATGGCCGCCTCTTGCTGGAAATGGCTTCTGCTGTTCCA
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttattttta-atgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
|| || || | ||| || | | |||| || | ||| || ||| | | | || | || || | | |||||| |||||||||||||||||| || || || |||||||| ||||||||||||| ||||| || |||||||| |||| || ||| | || |||| || |||||||
-----------------------------------------------------gtatgtggtatataaaaa----gaat--cctgaac---acttaacttattttttaattttatatgtcttgacattattggttgttttctt-tttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatct--ccgat-----ttgcttgaaagtgacctcttttacttcccc--ctttgttttatttttaatgtttaat-cggtttctt---gtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
| || ||| ||| | || ||| | | ||| || || || | | |||| | || || ||| | | | ||||| || ||||||| || | | || ||| | |||||| ||||||||| |||||||| || ||||| |||||||||||||||||||||| ||||| |||||||||||||| || ||| || |||| |||| || ||||||||
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttacttccccctttgttttatttttaatgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
tttcttgtttc CT-rich tract
tttgttttatttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttatttttaatgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA