Sequence
atgc intronic sequence ATGC exonic sequence...ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagcttttgccatagttggtccatgacaaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA02G42560.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 7
ggaaacataatatgaaaccattcacacatcttca---cttcacctatcaacttaagcttttgccatagttggtccatga--caaacattactg-----atttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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---------attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatggataaatcattcctctgttcactcgttcttcctatcatttattt-cagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 7
ggaaacataatatgaaaccattcacacatcttca---cttcacctatcaacttaagcttttgccatagttggtccatga--caaacattactg-----atttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
|| | |||||| | | | | | | | || | | | || | | ||| || | || | |||| || ||||||| ||| ||| | ||||| ||||||||||| |||||||||||||||||| ||||||||||| || |||||||||
---------attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatggataaatcattcctctgttcactcgttcttcctatcatttattt-cagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTCTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 7
ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagcttttgccatagttggtcc-atgac-aaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| | || || | || | | ||| | | || | || ||| ||| ||| | | || || ||||||| |||||||||||||| || || || ||||| || ||||||||||||||||||||||||||||| || |||||||||
---------------gttagcttaaactactgctctatattt-tcatggttattgttagttggtattagtctgatgtttaaaggtgggcggctttttttcagGGAAACCATCATTTACAAAAAAGCAGGCAGATCTCTTTTTCCCCCCAGATTTTGCTGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
---ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagctttt---gccatagttggtccatgac-aaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| | | |||| || || | | || | || ||| | ||| | || | || ||| || ||||| || ||||| || |||||||||||||| |||||||| ||||| || || ||||| |||||||||||||||||||| ||||||||||||
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 7
----ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagcttttgccatagttggtccatgacaaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
|| || || |||| | ||| || | | || | || || || || ||| | ||| | | | |||| || |||||||| ||| ||||||||||||||| |||||||||||||| || ||||||||||||||||||||||||||||| ||||||
gactcactactcttggtggaatcattatgttaccttttattttgttttgaatt----ctgttcttatgtttattcctgttctaacttcaataatttcttagcagGGAAACCAGGATTTACAAAGAAACAGGCTGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttaagcttttgccatagttggtccatgacaaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
tactgat putative branch site (score: 2)
aaacatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagcttttgccatagttggtccatgacaaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-gaaacata
- - - - - - tgaaacc
- - - - - - - - - - - cacacat
- - - - - - - - - - - - - - - - - cttcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat