Sequence
atgc intronic sequence ATGC exonic sequence...atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 7
--atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctg--gaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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attccaccccattcttctccttgtaggccat---taacagtgaataaatgttcatg-gataaatcattcctctgttcactcgttcttcctatcatttatttcagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 7
--atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctg--gaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
||||| | || ||| || | | || | || || | | |||||| | |||| | | ||| | | || || ||||||| ||| ||| | ||||| ||||| ||||| ||||| |||||||||||| ||||||||||| || |||||||||
attccaccccattcttctccttgtaggccat---taacagtgaataaatgttcatg-gataaatcattcctctgttcactcgttcttcctatcatttatttcagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTCTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 7
atagatatattctattatcactaaatcata-tatataattctatcatctttgatttggttaatcatccttctggaatttaactttcca-aatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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-------------gttagcttaaactactgctctatattttcatggttattg--ttagttggt-attagtctgatgtttaaaggtgggcggctttttttcagGGAAACCATCATTTACAAAAAAGCAGGCAGATCTCTTTTTCCCCCCAGATTTTGCTGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| | ||| | | || | ||||| | || | | | | || || ||| | | | || | |||| |||||||| || |||||||||||||| |||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgtt-ttctaggttgtattcatctgatctttaaaggttggc------gatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 7
atagatatattctattatcacta-aatcat-atatataattctatcatcttt--gatttggttaat-catccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| ||| | | | |||||| || | || ||| | ||| ||| ||| | | | | |||||| |||||||| |||||||| ||| ||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| ||||||
-----gactcactactcttggtggaatcattatgttaccttttattttgttttgaattctgttcttatgtttattcctgttctaacttcaataatttcttagcagGGAAACCAGGATTTACAAAGAAACAGGCTGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgatttggttaatcatccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
atttaac putative branch site (score: 3)
tttctttgc putative PPT
aatttaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttcca