Sequence
atgc intronic sequence ATGC exonic sequencegtattgcaatcttgtatgattattctctctcctggtgtgtgagaatcataatatgtaacttctatctctgactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA07G26540.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 5
-------------------------------------gtattgcaatcttgtatgattattctctctcctggtgtgtgag-aatcataatatgtaacttctatctctgactttgccatcaacttcct---cagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
| || | | || ||| | | ||| | | || || || | | | | ||| | || || | || | ||||||||||||||||| || ||||| ||||| | || ||| | ||||| ||||||||||| | ||||||||| |||||| | ||||||||||| ||| ||
gtaagtgggtgcatgcagtttattctctatcatgaaaacacaataacttggcattccaattgaatagtttagtgcctaattgattattat-tattattattattattattattattattattttgcattgcagGAAGAAAATAAAATCTTAGACAAGCTGCATCGCCAAAAGATTGCAGAAGTTGAAAAGCTGAGCCAAACTGTGAGAGAGTTGGAAGAGGCTGTTCTTCAAG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 1
----------gtattgcaatcttgtatgattattctctctcctggtgtgtgagaatcataatatgtaacttctatctctgactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
|| | || | | || | || | | | ||| | ||||| | | ||| | | |||| | | |||||||| || ||||| ||||| | |||||| | ||||| || || ||||||||||||||||| || ||||| |||||||||||||| |||| ||||| |
gtacgcgacagtggagatattcattgacactagtaactttaccagcttgtttgc-ccataa---gctaacagtatatgaggctttcctgttgcaccaaacagGAAGAGAACAAAATCTTGGATAGAATGCACCGCCAGAAAGTTGCTGAGGTTGAAAAGCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgcaatcttgtatgattattctctctcctggtgtgtgagaatcataatatgtaacttctatc--tctgactt-tgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
|| | || | ||| ||| | | | | |||| | | | | | ||||| | || || | |||||||||| |||||| | || | ||||||||| |||||||| || || || |||||||| || || || || ||||||||||||||||||| |||||||
----------gttctgtggtcgccatcttgttctttgtattt-acttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
gtattgcaatcttgtatgattattctctc-tcctggtgtgtgagaatcata-atatgtaacttctatctc--------tgactttgc---------catcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
| | | ||| ||| | | | | ||| ||||| || | | ||| | | | || | || ||| | ||||||| |||| |||| | ||||| ||||| ||||||||||| ||||| ||||||||||| | || | |||| | || ||||||| ||||| ||||| |
-----gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtattgcaatcttgtatgat----tattctctctcctggtgtgtgagaatcataatatgtaa-cttctatctctgactttgc-----------catcaacttcctc--------agGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
| | || | |||| || | || ||| | | ||| | || | | | ||||| |||| | | | || || |||| | | | |||||||||||||||||||||| || |||||| | || ||||| |||||||||||||| || ||||||||||| || ||||| ||||||||||| || || |
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgagaatcataatatgtaacttctatctctgactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
ctctgac putative branch site (score: 3)
cttcctc putative PPT
aatcataatatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgcaatcttgtatgattattctctctcctggtgtgtgagaatcataatatgtaacttctatctctgactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG