Sequence
atgc intronic sequence ATGC exonic sequence...gaaagttctacgaatttacgtaaactctcgagttagacaactttgctactacatgataattgagatattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
Basic information
species | Glycine max |
transcript | GLYMA18G45720.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G60950.1 (Arabidopsis thaliana), 3'ss of exon 6
gaaagttctacgaatttacgtaaactctcgagttaga--caactttgctacta-catgataattgagatatttt-cactgactttttcattaa---catctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
|| | | | | || || | ||| || |||| || || ||| || | | | || || |||| | |||| || |||||||| || ||||||||||||||| |||||||||| ||||||| || || ||| |||||||| | || | ||||||||||
----gtacacttgctctgtaaagggtccagaataagatgcatttttgttattatcattttatatctcctgtcttacaatgaccaactatttaaatgttctcaaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTCCGTGGAAGCTTAACAGCAATTCCTGGACTATCTGCTATGATTGAT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 7
gaaagttctacgaatttacgtaaactctcgagttagacaactttgc--tactacatgataattgagatattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
| | | | | | | || | | || || | | || || || | || ||| ||| | | | || || |||||||| || ||||||||||||||| ||||||||||||||||||| || || ||| |||||||| | || ||||||||||||
gtacacttttcctgtaaaggtccagaataagattcatttttcttatatcattttatatctcctgtcttacaatgaccaactatttaaatgatctc-aaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTTGGTGGAAGCTTAACAGCAATTCCTGGACTATCTGATATGATTGAT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 6
gaaagttctacgaatttacgtaaactctcgagttaga--caactttgctacta-catgataattgagatatttt-cactgactttttcattaa---catctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
|| | | | | || || | ||| || |||| || || ||| || | | | || || |||| | |||| || |||||||| || ||||||||||||||| |||||||||| ||||||| || || ||| |||||||| | || | ||||||||||
----gtacacttgttctgtaaagggtccagaataagatgcatttttgttattatcattttatatctcctgtcttacaatgaccaactatttaaatgttctcaaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTCCGTGGAAGCTTAACAGCAATTCCTGGACTATCTGCTATGATTGAT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 7
---gaaagttctacgaatt--tacgtaaactctcgagttagacaactttgctactacatgataattgagatattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
| | || | | || | | | | | || | ||| | | || || | | ||| | || | ||||| | | | |||||||||||||| ||||||||||| ||| |||||||||||||||||||||| || || || ||||||||||||||||||||||||
ttccagtatatcacaagctagtagatctattttgtaatt-gttaacactttaatta-attacagttg---ttttggaattgactaatactcgtttgttcaatcagCCAAAGCCAAGAATTGATTATACTCTGAAGGCTGTTGGTGGAAGTTTAACAGCTCTCCCTGGAATTTCAGATATGATTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctactacatgataattgagatattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
cattaac putative branch site (score: 2)
ataattgagatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaagttctacgaatttacgtaaactctcgagttagacaactttgctactacatgataattgagatattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTTCCTGGAATTTCAGATATGATTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - -catgata