Sequence
atgc intronic sequence ATGC exonic sequencegtaagttattcttcaccaaaaaaccatagcaccaatttcagtagtacttctagatcactgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
Basic information
species | Glycine max |
transcript | GLYMA07G36000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 5
gtaagt-tattc-ttcaccaaaaaaccatagcaccaatttc------agtagta--cttctagatcac-----tgttatttacagaca-tggattttctcattcttctacaaatta--cagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
|||||| | | || | | | || ||| ||| || || ||| || || || | || || | | | ||| | | | || || ||||| || || || || || |||||||| |||||||||||||||||||| || || ||||| |||||||| ||| ||||||| || |||||||| || || |
gtaagtgtgcacactctcttgggggctttggcttttctttgtatccgagttgtgatctgctacatggtataggtgcaatgcttaatcactgcaatgttaaattttgttgcgaaatattcagGCCGACGCGGACGGGAACGGAACCATCGATTACGACGAGTTCATCACAGCGACGATGCACATGAACAGGATGGACAGAGAGGAGCATCTTTACACCGCGT
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g04170.1 (Oryza sativa), 3'ss of exon 3
gtaagttattcttcaccaaaaaaccatagcaccaatttcagtagtacttctagatcac-tgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
|| | || ||| || | | | || | |||||| || |||| | || || || |||| | | | | | | ||| || ||||||||||||||||||||||||| || || || || |||||| ||||||| ||| |||| ||||||| |||| | ||||||| || ||||| || || |
----gtgagtcctcatagtgaagctacaa-acttagttcagt------tcgagatgaaatgctaaa-actgacaggactcctggaaattcctttcaactttcagGCTGATGCTGATGGCAATGGAATTATCGACTATGAGGAGTTCGTCACCGCGACAGTGCACATGAACAAAATGGATCGAGAAGAGCACCTTTACACGGCAT
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 5
gtaagttattcttcaccaaaaaaccatagcaccaatttcagtagtacttctagatcactgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
||||| | | | | | || | | || || | ||| ||| | | | | | | || | || ||| |||||||||||| || ||||| || || || |||||||| ||||||||||| || || ||||| |||||||| ||| |||| || || || || || || || |
gtaaggatagccacgcttaccaga-atcatatggaattgtacttcacattcagaaaactttcagacttacaaaatgtttgtggatttggggggaaaaaaacagGCTGATGCAGACGGCAACGGGACAATCGATTACGAGGAGTTCATCACTGCGACGATGCACATGAACAGGATGGACAGGGAGGAGCACCTCTACACCGCGT
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g03970.1 (Oryza sativa), 3'ss of exon 3
gtaagttattcttcaccaaaaaaccatagcaccaatttcagtagtacttctagatcac-tgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
|| | || ||| || | | | || |||||| | ||| |||| | || || || |||| | | | | | | ||| || ||||||||||||||||||||||||| || || || || |||||| ||||||| || |||| ||||||| |||| | ||||||| || ||||| || || |
----gtgagtcctcatagtgaagctaca-----aacttcagtt-cagttcgagatgaaatgctaaa-actgacaggactcctggaaattcctttcaactttcagGCTGATGCTGATGGCAATGGAATTATCGACTATGAGGAGTTCGTCACCGCGACGGTGCACATGAACAAAATGGATCGAGAAGAGCACCTTTACACGGCAT
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttattctt---caccaaaaaaccatagcaccaatttcagtagtacttctagatcactgttatttacagacatggattttctcattctt----ctacaaat-tacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
|| ||| ||||| | || | |||| | | | | ||| | | || ||||| | || || || || ||||||||||||||||||| |||||||| || || || | |||||| ||| | || |||||||| || |||||| | ||||||||||||||||||| | ||||
gtgagtccttcttgtacttgcaagagatttagctttagtcaaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttattcttcaccaaaaa--accatagca-----------ccaatttca-gtagtacttctagatc---actgttatt-tacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
||||||| | | ||||||| | | || | ||| || ||| || | ||| |||| | | || | | ||| | | | ||| | ||| | |||||||||| |||||||||||||||||||| || || ||||| ||||| ||||||||||| ||||||||||| ||| |||||| |||||||| || ||||
gtaagttctcaccccccaaaaatgatctcagtgaagttcttttgcagattacatgtaaattttttcgatttcagctgtcactctaataattttgatgctttttattttccataaa--aaagGCTGATGCAGATGGCAATGGAACCATTGACTATGATGAGTTTATCACGGCAACAATGCACCTGAACAGAATGGACAAAGAAGACCATCTTTACACAGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctagatcactgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
ttttctcattcttcta CT-rich tract
tgttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttattcttcaccaaaaaaccatagcaccaatttcagtagtacttctagatcactgttatttacagacatggattttctcattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC