Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
Basic information
species | Glycine max |
transcript | GLYMA10G00880.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
gtaaagaatatgccgagactaga-tgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
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--------tctgttccgtccaatctatgcctttcaaaa--aaaatgttttca--agtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
gtaaagaatatgccgagactagatgcgatcttaaacat--caacatatcctcgtt---aatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
| | | || | || | || |||| ||| | ||| || | | ||| || | | | || | | | | | || ||||| ||||| || |||||| | || | |||| |||||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||| |||
----------------ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
gtaaaga-atatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcat-gttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
||| | | |||| ||| || | || | || | || || || || ||| | | | | | || || || ||| | | || |||||||| || || |||||| | || | |||| || ||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||| |||
-taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgat-----tgcatccttgctgagctgtatccgat---ccacattttttt----ttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgtt-catcagtgtctaataatttctgtttc---tatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
| | | | | || | | | || | | | || | || | | || |||| || | | || | | | | || ||||||||||| || |||||| | || | |||| || ||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||| |||
---------------taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgattgcatccttgctgagctgtatccgacccacaattttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtc-taataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
| ||| | || | | | || ||| || | || | ||| ||| ||| | |||| |||| || ||||| |||||| | ||||||||||| |||||||||| || || || || || || ||||||||||||||||||||||| ||||||||| |||
------------------------------gtgtctatcgatatgttat-acagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
||| | | | | | | || | | | | | | | | || || | || || | ||| | | ||| | || | || ||| |||| |||||||||||||| |||| |||||||| |||||||||||||| || || ||||| ||||||||| | ||||||||||| |||||||||||| |||
---------gtgct-atatttgctttcttgttttgctttgatttgtgattggtt-cctggttacattgtcttgat-attgttttgttctttgtattgatttg-cgtt-tagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgttt----ctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
| | || | | || | | | ||| || | | || | | |||| ||| | || | |||||| |||| || ||||||||| | ||||||||||| || ||||||||||| || || || || ||||||||||||||||| ||||||||||| |||||| |||
------------------------------------gtgagaatgtgc--gtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
gtctaat putative branch site (score: 3)
taataatttctgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT