Sequence
atgc intronic sequence ATGC exonic sequencegtattagtcttatttgtgattaaaaaaaatagtgtatattatcatagtacactggacatatggaatgatatgcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
Basic information
species | Glycine max |
transcript | GLYMA12G35840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 6
gtattagtcttatttgtgattaaaaaaaatagtgtatattatcatagtacactggacatatggaatgata--tgcaaattaaatatgg--tacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
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gtat--gttacatctatcat--------atcatgtttgcaa-catagttaattaat--tgtgaaattatggttttaatattgatgtggactacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGACGTATGCCTGTTAGCTAGAATGATGGCTGCTAACTTATACTATGCACAGATAGAGGATCTGATGTT
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
gtattagtcttatttgtgattaaaaaaaatagtgtatattatc---atagtacactgg--acatatggaatgatat-gcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
| | ||| || | | | || ||||| || | || ||| || | | ||| | | ||| ||||||||||| || || ||||| ||||||||||| ||||| | ||||||||||||||| | ||||| || | || || || || ||||| |||||
-----------------gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcac-caatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
------------gtattagtcttatttgtg------attaaaaaaaatagtgtatattatcatagtacactggacatatggaatgatatg----caaattaa-atatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
| | |||||||| ||| | | || | |||| ||| || | | | |||| || | | | ||||| ||||||||||| || || || || ||||||||||| ||||| |||||||||||||||||||||||||||||| || ||||||||||||| || |||||
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 4
gtattagtcttatttgtgattaaaaaaaatagtgta-tatta-tcatagtacactggacata--------tggaatgatatgcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
||| || | ||| | | | | |||| | || | | |||| | | |||| |||| | | |||| | | || | ||||||| ||||| || |||||||| || ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||| |||||||||||
taatttatcaaagttg-agtcagactcattagttgactaccagttatagaaagcaggactctctctcccctggattaacatgcttttgacatgaaatgcagGTAACCCAAGGGTGACTCCTGAGGTCACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTATACTATTCCCAGATAGAGGATCTTATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattatcatagtacactggacatatggaatgatatgcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
aatgatatgcaaatta 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
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gtattagtcttatttgtgattaaaaaaaatagtgtatattatcatagtacactggacatatggaatgatatgcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT