Sequence
atgc intronic sequence ATGC exonic sequencegtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
Basic information
species | Glycine max |
transcript | GLYMA08G01880.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 8
---------gtcagaatgatttctacatccattcaacacttt------ttgttgcagatgctttgtctgtagt--------atattcttatctttgtcac---tgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
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gtaatgaaaatcctacattcttctacacttctctagttatttgatgaatttatgcctatcttctctccgctGTTATAAAAATCAACCTTGCTTCTCTCACACATGTAATAACTATGCAGGTTATAAAAAATTCTAATGGATGTAATCTTGCTGTTGACATATGGAGCTTAGGATGCACGGTTTTAGAGATGGCTACCTCAAAACCACCATGGAGCCAAT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
gtcagaatgatt-tctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
|| | ||| ||| | || || ||| | | || || | || | | | ||| | ||| || ||| ||||||||||||| |||||||| || || || || ||||| ||||||||| | ||||||||||| |||||||||| ||| | ||||| || |||||||| |
gtatcactgaaaatctttacttgtt-aattttttgtttcatgcatatcttat-tgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 8
--gtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgt---cactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
| | | | | ||| ||| | ||| ||| || | | || ||| || | ||||| || ||| || |||||||||||||| | | ||| ||||| ||||| ||||||||||||||| |||||||||| || | |||||||| || ||||||| || ||||||||||
gtattaccccaaatcttgcatt-gttctgctactttagttattttggccagatttata---tatcctgacctttgcttatgttgtgacaaatatgcagGTTATAAAAAATGCTAGTGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAAT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 7
--gtcagaatgatttctacatc--cattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
| | | | ||| | | ||| | || || | || || | | || | || | | | || ||| || |||||||||||||| | | || ||||| ||||| ||||||||||||||| |||||||||| || | |||||||| || ||||||| || ||||||||||
gtattgccccaaatcttgcattgtcccgctacattagttattttggttgggtt-tatatatcttgactttttttcttgtgttgtgacaaatatgcagGTTATAAAAAATGCTAGCGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAAT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 7
--gtcagaatgat-ttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcac--------------tgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
||||| ||| | | | | | ||||| || | | | || | | ||| | || | ||| | ||| || | |||||||||||||||| ||||| || || |||| |||||| ||||||||| |||| |||||||| |||| ||||| || |||| || || |||||||| |
gtactgaaatgaagctcttcctttagtttgtatttttttttttaa---ttcaatgtgcatcacattataatttctgttaacaaaatactaaccatgcagcacaaatgcagGTTATAAAAAATTCTAATGGATGCAACCTTGTGGTTGACATATGGAGTTTAGGTTGCACTGTCCTGGAAATGGCTACCTCAAAGCCACCATGGAGCCAGT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
||||| ||| | ||||| || || | | ||| | | || | | || ||||||| || | ||| || ||| ||||| ||||||||||| |||| |||||||| || ||||||||||| ||||| |||||||| || ||||| ||||| |||||||| |||||||| |
gtcagtatg-ctgctacaacctgtctgtttcaatgttgacaggcgttatgc---tgatgctttattatctt-------gcttggatttca--gGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 9
gtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
||||| || ||| | || ||| || || | | | ||| | | | | | | | | | | | || | || | |||| ||||| || |||||||| ||||||||||| || ||| |||||||||| || ||||| |||||||||||||| ||||||||||| ||||||||||| |
gtcagcctggttttcat-----ttttgtactgttggtcactgtt--cttgacaatcctttctagtaacatatttgattgaatttatcattcagGTCATAAAGAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
tatattcttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG